From cf71de617d4e5bc8ff15fa3df522c6b6580ed6e4 Mon Sep 17 00:00:00 2001 From: BorisYourich Date: Wed, 21 Jun 2023 14:24:05 +0200 Subject: [PATCH 1/8] changed passwords, fixed ansible gathering facts issue --- .github/workflows/ci.yaml | 1 + ansible.cfg | 1 + group_vars/galaxyservers.yml | 19 ++++-- group_vars/secret.yml | 68 +++++++++++-------- hosts | 6 +- roles/galaxyproject.tusd/defaults/main.yml | 2 +- .../galaxy/config/oidc_backends_config.xml | 4 +- 7 files changed, 59 insertions(+), 42 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index b4daac2..9798bbf 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -23,6 +23,7 @@ jobs: - name: Copy files to test instance and preserve secrets and hosts run: | rsync -rav * debian@usegalaxy-test.cerit-sc.cz:~/usegalaxy-${{ steps.date.outputs.date }} + ssh debian@usegalaxy-test.cerit-sc.cz 'cp ~/usegalaxy/group_vars/secret.yml ~/usegalaxy-${{ steps.date.outputs.date }}/group_vars' ssh debian@usegalaxy-test.cerit-sc.cz 'cp ~/usegalaxy/hosts ~/usegalaxy-${{ steps.date.outputs.date }}' ssh debian@usegalaxy-test.cerit-sc.cz 'cp ~/usegalaxy/.vault-password.txt ~/usegalaxy-${{ steps.date.outputs.date }}' - name: Run playbook diff --git a/ansible.cfg b/ansible.cfg index 2e42374..bc40777 100644 --- a/ansible.cfg +++ b/ansible.cfg @@ -3,6 +3,7 @@ interpreter_python = /usr/bin/python3 inventory = hosts retry_files_enabled = false vault_password_file = .vault-password.txt +gather_subset=!hardware no_log = True # Show diffs of changes diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index ffbfd2c..06944ae 100644 --- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -7,7 +7,7 @@ galaxy_manage_cleanup: true galaxy_layout: root-dir galaxy_root: /srv/galaxy galaxy_user: {name: "{{ galaxy_user_name }}", shell: /bin/bash} -galaxy_commit_id: 7a9ba0c6529d72517c7627422eac16eadff15b46 # release_23.0 +galaxy_commit_id: release_23.0 # 7a9ba0c6529d72517c7627422eac16eadff15b46 galaxy_force_checkout: true miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda" miniconda_version: 4.12.0 @@ -109,9 +109,12 @@ galaxy_config: admin_users: - admin@example.org - 499542@muni.cz + - 325073@mail.muni.cz + - demko@cesnet.cz + allow_user_creation: False database_connection: "postgresql:///{{ galaxy_db_name }}?host=/var/run/postgresql" - file_path: /data/datasets - job_working_directory: /data/jobs + file_path: /mnt/data/datasets + job_working_directory: /mnt/data/jobs object_store_store_by: uuid id_secret: "{{ vault_id_secret }}" job_config: "{{ galaxy_job_config }}" # Use the variable we defined above @@ -158,7 +161,7 @@ galaxy_config: statsd_host: localhost statsd_influxdb: true # FTP - ftp_upload_dir: /data/uploads + ftp_upload_dir: /mnt/data/uploads ftp_upload_site: "{{ inventory_hostname }}" gravity: process_manager: systemd @@ -228,7 +231,7 @@ galaxy_config_templates: dest: "{{ galaxy_config_dir }}/oidc_backends_config.xml" galaxy_extra_dirs: - - /data + - /mnt/data - "{{ galaxy_config_dir }}/{{ tpv_config_dir_name }}" galaxy_extra_privsep_dirs: @@ -327,6 +330,7 @@ rabbitmq_config: rabbitmq_vhosts: - pulsar + - galaxy_gpu - galaxy_internal rabbitmq_users: @@ -337,6 +341,9 @@ rabbitmq_users: - user: pulsar password: "{{ rabbitmq_users_password.galaxy }}" vhost: pulsar + - user: galaxy_gpu + password: "{{ rabbitmq_users_password.galaxy_gpu }}" + vhost: galaxy_gpu - user: galaxy password: "{{ vault_rabbitmq_password_galaxy }}" vhost: galaxy_internal @@ -347,7 +354,7 @@ rabbitmq_users: # TUS galaxy_tusd_port: 1080 -galaxy_tus_upload_store: /data/tus +galaxy_tus_upload_store: /mnt/data/tus #Redis galaxy_additional_venv_packages: diff --git a/group_vars/secret.yml b/group_vars/secret.yml index 9fee46e..ac9fff7 100644 --- a/group_vars/secret.yml +++ b/group_vars/secret.yml @@ -1,31 +1,39 @@ $ANSIBLE_VAULT;1.1;AES256 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diff --git a/hosts b/hosts index ad383aa..81236a7 100644 --- a/hosts +++ b/hosts @@ -1,9 +1,9 @@ [galaxyservers] -usegalaxy-test.cerit-sc.cz ansible_connection=local ansible_user=debian +galaxy-cz.grid.cesnet.cz ansible_connection=local ansible_user=debian [dbservers:children] galaxyservers [monitoring] -usegalaxy-test.cerit-sc.cz ansible_connection=local ansible_user=debian +galaxy-cz.grid.cesnet.cz ansible_connection=local ansible_user=debian [sentryservers] -usegalaxy-test.cerit-sc.cz ansible_connection=local ansible_user=debian +galaxy-cz.grid.cesnet.cz ansible_connection=local ansible_user=debian diff --git a/roles/galaxyproject.tusd/defaults/main.yml b/roles/galaxyproject.tusd/defaults/main.yml index 3fa7cf5..3633d0b 100644 --- a/roles/galaxyproject.tusd/defaults/main.yml +++ b/roles/galaxyproject.tusd/defaults/main.yml @@ -2,7 +2,7 @@ # Use 'latest' to install the latest (stable) release from https://github.com/tus/tusd/releases/, or a valid tag for a # specific tagged release (e.g. v1.7.3) -tusd_version: v1.8.0 # latest +tusd_version: v1.6.0 # Path of the tusd binary tusd_path: /usr/local/sbin/tusd diff --git a/templates/galaxy/config/oidc_backends_config.xml b/templates/galaxy/config/oidc_backends_config.xml index 6ec05c7..ac19887 100644 --- a/templates/galaxy/config/oidc_backends_config.xml +++ b/templates/galaxy/config/oidc_backends_config.xml @@ -1,8 +1,8 @@ - 0740f7cc-4573-4a5f-9810-6fd9e57cf6be - 42effa24-73ba-4c05-b3f9-6e75bb3438c171c54b5d-eb9b-441a-8fdf-ab14d5caac9e + {{ e_infra_client_id }} + {{ e_infra_client_secret }} https://usegalaxy-test.cerit-sc.cz/authnz/keycloak/callback https://login.e-infra.cz/oidc https://www.e-infra.cz/img/logo.svg From 5cbebcb5fe71cf257aa4bacd2724d8f607829006 Mon Sep 17 00:00:00 2001 From: BorisYourich Date: Wed, 21 Jun 2023 16:08:47 +0200 Subject: [PATCH 2/8] updates --- group_vars/galaxyservers.yml | 25 +++++++++++++++++++++++-- 1 file changed, 23 insertions(+), 2 deletions(-) diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index 06944ae..6a50044 100644 --- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -21,14 +21,34 @@ galaxy_job_config: workers: 4 pulsar_runner: load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner - galaxy_url: "https://{{ inventory_hostname }}" - amqp_url: "pyamqp://pulsar:{{ rabbitmq_users_password.galaxy }}@{{ inventory_hostname }}:5671/pulsar?ssl=1" + galaxy_url: "https://{{ rabbitmq_hostname }}" + amqp_url: "pyamqp://galaxy:{{ rabbitmq_users_password.galaxy_gpu }}@{{ rabbitmq_hostname }}:5671/galaxy_gpu?ssl=1" amqp_acknowledge: true amqp_ack_republish_time: 1200 amqp_consumer_timeout: 2 amqp_publish_retry: true amqp_publish_retry_max_retries: 60 manager: _default_ + pulsar_gpu_runner: + load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner + galaxy_url: "https://{{ rabbitmq_hostname }}" + amqp_url: "pyamqp://galaxy_gpu:{{ rabbitmq_users_password.galaxy_gpu }}@{{ rabbitmq_hostname }}:5671/galaxy_gpu?ssl=1" + amqp_acknowledge: true + amqp_ack_republish_time: 1200 + amqp_consumer_timeout: 2 + amqp_publish_retry: true + amqp_publish_retry_max_retries: 60 + manager: drmaa_gpu + # pulsar_runner: + # load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner + # galaxy_url: "https://{{ inventory_hostname }}" + # amqp_url: "pyamqp://pulsar:{{ rabbitmq_users_password.galaxy }}@{{ inventory_hostname }}:5671/pulsar?ssl=1" + # amqp_acknowledge: true + # amqp_ack_republish_time: 1200 + # amqp_consumer_timeout: 2 + # amqp_publish_retry: true + # amqp_publish_retry_max_retries: 60 + # manager: _default_ handling: assign: ['db-skip-locked'] execution: @@ -303,6 +323,7 @@ nginx_conf_ssl_certificate_key: /etc/letsencrypt/live/{{ inventory_hostname }}/p pip_install_packages: - name: docker # RabbitMQ +rabbitmq_hostname: "{{ inventory_hostname }}" rabbitmq_container: name: rabbit_hole image: rabbitmq:3.11-management From e10aba7eee8dff9a741e6132434663ee1a73f8ae Mon Sep 17 00:00:00 2001 From: root Date: Wed, 6 Sep 2023 13:46:20 +0200 Subject: [PATCH 3/8] sync with production version --- eu_tool_list.yaml | 8417 +++++++++-------- files/galaxy/config/tpv_rules_local.yml | 80 +- files/galaxy/tools/testing.xml | 11 +- files/galaxy/welcome.html | 37 +- galaxy.yml | 21 + group_vars/galaxyservers.yml | 71 +- group_vars/secret.yml | 81 +- hosts | 6 +- roles/galaxyproject.nginx/tasks/apt.yml | 10 +- roles/galaxyproject.tusd/defaults/main.yml | 2 +- .../usegalaxy_eu.certbot/tasks/renew-cron.yml | 2 +- .../galaxy/config/object_store_conf.xml.j2 | 14 + .../galaxy/config/oidc_backends_config.xml | 9 +- templates/nginx/galaxy.j2 | 24 +- 14 files changed, 4704 insertions(+), 4081 deletions(-) create mode 100644 templates/galaxy/config/object_store_conf.xml.j2 diff --git a/eu_tool_list.yaml b/eu_tool_list.yaml index 7015f16..16d6328 100644 --- a/eu_tool_list.yaml +++ b/eu_tool_list.yaml @@ -5,18 +5,11 @@ tools: - 7ed6dda64a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu -- name: dbbuilder - owner: galaxyp - revisions: - - 983bf725dfc2 - tool_panel_section_label: Get Data - tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: + - 6ea73833cf67 - f5ea3ce9b9b0 - - 83c7d564b128 - - 69ebb7f46e45 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download @@ -28,15 +21,9 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 265c35540faa + - a371252a2cf6 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu -- name: spocc_occ - owner: ecology - revisions: - - f9d76a46799a - tool_panel_section_label: Animal Detection on Acoustic Recordings - tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: @@ -160,7 +147,13 @@ tools: - name: ega_download_client owner: iuc revisions: - - 9564758e8638 + - f9db47f68e5e + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: dbbuilder + owner: galaxyp + revisions: + - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_datasets @@ -172,7 +165,13 @@ tools: - name: pysradb_search owner: iuc revisions: - - f63cf0adfd87 + - b91e1e70f3a1 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: spocc_occ + owner: ecology + revisions: + - f64b3c1a80a6 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ena_upload @@ -208,7 +207,7 @@ tools: - name: unzip owner: imgteam revisions: - - 38eec75fbe9b + - 57f0914ddb7b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -223,12 +222,42 @@ tools: - 3ddd99c7efee tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu -- name: filter_tabular +- name: gff3_rebase owner: iuc revisions: - - 4d5aae46f850 + - f7ad5e69aa60 + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: basecoverage + owner: devteam + revisions: + - 9c5ff4695c97 + tool_panel_section_label: Operate on Genomic Intervals + tool_shed_url: toolshed.g2.bx.psu.edu +- name: subtract + owner: devteam + revisions: + - 7a2a604ae9c8 + tool_panel_section_label: Join, Subtract and Group + tool_shed_url: toolshed.g2.bx.psu.edu +- name: coverage + owner: devteam + revisions: + - bc9c66c1e9c9 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu +- name: cluster + owner: devteam + revisions: + - a126ec6ea0e4 + tool_panel_section_label: Operate on Genomic Intervals + tool_shed_url: toolshed.g2.bx.psu.edu +- name: imagecoordinates_flipaxis + owner: imgteam + revisions: + - f8f1100d0701 + tool_panel_section_label: Imaging + tool_shed_url: toolshed.g2.bx.psu.edu - name: dna_filtering owner: devteam revisions: @@ -241,6 +270,42 @@ tools: - 6595517c2dd8 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu +- name: merge + owner: devteam + revisions: + - 0926c81f382c + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: intersect + owner: devteam + revisions: + - 8ddabc73af92 + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: flanking_features + owner: devteam + revisions: + - 8307665c4b6c + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: get_flanks + owner: devteam + revisions: + - 4cd116158aef + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: complement + owner: devteam + revisions: + - e0a23ab32d7f + tool_panel_section_label: Operate on Genomic Intervals + tool_shed_url: toolshed.g2.bx.psu.edu +- name: subtract_query + owner: devteam + revisions: + - 960d5d114184 + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu - name: diff owner: bgruening revisions: @@ -271,12 +336,6 @@ tools: - dd40b1e9eebe tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu -- name: imagecoordinates_flipaxis - owner: imgteam - revisions: - - f8f1100d0701 - tool_panel_section_label: Imaging - tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: @@ -286,7 +345,7 @@ tools: - name: regex_find_replace owner: galaxyp revisions: - - 399da6b5ec21 + - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: join_files_on_column_fuzzy @@ -298,8 +357,8 @@ tools: - name: text_processing owner: bgruening revisions: - - f46f0e4f75c4 - d698c222f354 + - f46f0e4f75c4 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular @@ -320,52 +379,34 @@ tools: - b722161a845a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu -- name: jq +- name: filter_tabular owner: iuc revisions: - - 5ff75eb1a893 + - 4d5aae46f850 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu -- name: reshape2_cast +- name: prinseq owner: iuc revisions: - - d3b66a3a08ca + - 1ee282794de3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu -- name: reshape2_melt +- name: jq owner: iuc revisions: - - 317ed0ee8bf2 + - 5ff75eb1a893 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu -- name: basecoverage - owner: devteam - revisions: - - 9c5ff4695c97 - tool_panel_section_label: Operate on Genomic Intervals - tool_shed_url: toolshed.g2.bx.psu.edu -- name: subtract - owner: devteam - revisions: - - 7a2a604ae9c8 - tool_panel_section_label: Join, Subtract and Group - tool_shed_url: toolshed.g2.bx.psu.edu -- name: prinseq +- name: reshape2_cast owner: iuc revisions: - - 1ee282794de3 + - d3b66a3a08ca tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu -- name: cluster - owner: devteam - revisions: - - a126ec6ea0e4 - tool_panel_section_label: Operate on Genomic Intervals - tool_shed_url: toolshed.g2.bx.psu.edu -- name: gff3_rebase +- name: reshape2_melt owner: iuc revisions: - - f7ad5e69aa60 + - 317ed0ee8bf2 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -380,12 +421,6 @@ tools: - 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iuc revisions: - d6255614afd7 @@ -1038,64 +1031,124 @@ tools: - 953b4821b183 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: flash +- name: fastq_groomer + owner: devteam + revisions: + - 47e5dbc3e790 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_manipulation + owner: devteam + revisions: + - 5b87038565bb + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_masker_by_quality + owner: devteam + revisions: + - 9dfda4e310ed + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ucsc_fasplit owner: iuc revisions: - - 01a4ebf1f237 + - bf04bd405d5b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: mqc - owner: rnateam +- name: fastq_paired_end_deinterlacer + owner: devteam revisions: - - 523dd2a71270 + - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: fasta_stats +- name: fastq_paired_end_interlacer + owner: devteam + revisions: + - 2ccb8dcabddc + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_paired_end_joiner + owner: devteam + revisions: + - c885369b207b + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_paired_end_splitter + owner: devteam + revisions: + - e39cc71d3ed6 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: pear owner: iuc revisions: - - 0dbb995c7d35 + - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: filtlong +- name: fastqe owner: iuc revisions: - - 41b2ad601cf0 + - 89d299153577 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastx_clipper +- name: seqkit_stats + owner: iuc + revisions: + - 54a954ee64d4 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: seqkit_fx2tab + owner: iuc + revisions: + - b1b12eaebfa9 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fasta_filter_by_length owner: devteam revisions: - - cb1e251cac37 + - 8cacfcf96a52 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: cutadapt - owner: lparsons +- name: fasta_to_tabular + owner: devteam + revisions: + - e7ed3c310b74 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: seqkit_locate + owner: iuc revisions: - - 135b80fb1ac2 + - 6510652376b1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastx_nucleotides_distribution +- name: tabular_to_fastq owner: devteam revisions: - - ad116ae3f4d9 + - 2dcfbbf9071a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastx_barcode_splitter +- name: tabular_to_fasta owner: devteam revisions: - - 4bedca26c133 + - 0a7799698fe5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: bctools_extract_crosslinked_nucleotides +- name: fasta_stats owner: iuc revisions: - - 66d1f96c5600 + - 0dbb995c7d35 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: ucsc_fasplit +- name: cutadapt + owner: lparsons + revisions: + - 8c0175e03cee + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bctools_extract_crosslinked_nucleotides owner: iuc revisions: - - bf04bd405d5b + - 66d1f96c5600 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: atactk_trim_adapters @@ -1164,12 +1217,6 @@ tools: - 9dad3d0b27bc tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: umi_tools_dedup - owner: iuc - revisions: - - f1d33e4c7bd8 - tool_panel_section_label: FASTA/FASTQ - tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: @@ -1188,12 +1235,6 @@ tools: - f82868a026ea tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: lighter - owner: bgruening - revisions: - - b0cfd92907eb - tool_panel_section_label: FASTA/FASTQ - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_join owner: lparsons revisions: @@ -1206,53 +1247,35 @@ tools: - ae4d5733272f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: gfastats - owner: bgruening +- name: seqcomplexity + owner: iuc revisions: - - 3ef480892a9f + - 054c3355458d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: rcorrector - owner: iuc +- name: fasta_regex_finder + owner: mbernt revisions: - - 6703b98884a2 + - 9a811adb714f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: pear +- name: bbtools_bbduk owner: iuc revisions: - - b4c6f054210a + - 159b04e36791 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: seqcomplexity +- name: bbtools_bbmerge owner: iuc revisions: - - 054c3355458d + - c05232655d00 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: seqkit_stats - owner: iuc - revisions: - - 54a954ee64d4 - tool_panel_section_label: FASTA/FASTQ - tool_shed_url: toolshed.g2.bx.psu.edu -- name: seqkit_fx2tab - owner: iuc - revisions: - - b1b12eaebfa9 - tool_panel_section_label: FASTA/FASTQ - tool_shed_url: toolshed.g2.bx.psu.edu -- name: adapter_removal - owner: iuc - revisions: - - 04d05400d3a6 - tool_panel_section_label: FASTA/FASTQ - tool_shed_url: toolshed.g2.bx.psu.edu -- name: seqkit_locate +- name: qualimap_counts owner: iuc revisions: - - 6510652376b1 - tool_panel_section_label: FASTA/FASTQ + - 1672b9bea89b + tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc @@ -1260,40 +1283,34 @@ tools: - abfd8a6544d7 tool_panel_section_label: Quality Control tool_shed_url: toolshed.g2.bx.psu.edu -- name: qualimap_counts - owner: iuc - revisions: - - 1672b9bea89b - tool_panel_section_label: RNA Analysis - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_info owner: bgruening revisions: - 7a821cd57b43 tool_panel_section_label: Quality Control tool_shed_url: toolshed.g2.bx.psu.edu -- name: bamtools_filter - owner: devteam +- name: samtools_view + owner: iuc revisions: - - 108db6635177 + - 5826298f6a73 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: pileup_interval +- name: samtools_reheader owner: devteam revisions: - - 9c1c0b947e46 + - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: pileup_parser - owner: devteam +- name: qualimap_bamqc + owner: iuc revisions: - - 85bedbea8a12 + - 4a89c6f84425 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: sam2interval +- name: sam_pileup owner: devteam revisions: - - 75557c0908a9 + - a3b4ad6858ff tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_merge @@ -1302,12 +1319,6 @@ tools: - 1977f1637890 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: sam_pileup - owner: devteam - revisions: - - a3b4ad6858ff - tool_panel_section_label: SAM/BAM - tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: @@ -1332,24 +1343,6 @@ tools: - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: samtools_view - owner: iuc - revisions: - - 5826298f6a73 - tool_panel_section_label: SAM/BAM - tool_shed_url: toolshed.g2.bx.psu.edu -- name: samtools_reheader - owner: devteam - revisions: - - bb8cfc6f6e0c - tool_panel_section_label: SAM/BAM - tool_shed_url: toolshed.g2.bx.psu.edu -- name: qualimap_bamqc - owner: iuc - revisions: - - 4a89c6f84425 - tool_panel_section_label: SAM/BAM - tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc owner: iuc revisions: @@ -1362,16 +1355,10 @@ tools: - ddb22028b552 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: tag_pileup_frequency - owner: iuc - revisions: - - 580e8bcb6413 - tool_panel_section_label: SAM/BAM - tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_markdup owner: iuc revisions: - - b5527cc104ab + - ce32171c6d44 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge @@ -1437,7 +1424,7 @@ tools: - name: samtools_coverage owner: iuc revisions: - - ae36fab06bc2 + - c4ff13d2aab3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: ngsutils_bam_filter @@ -1446,10 +1433,28 @@ tools: - 2e957d4c4b95 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: bamtools_split_mapped +- name: samtools_calmd + owner: devteam + revisions: + - 92ec40abcdcf + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bamhash + owner: bgruening + revisions: + - 63f6f42d112b + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: samtools_phase + owner: devteam + revisions: + - 1e5880498f52 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: mosdepth owner: iuc revisions: - - 6dbef7ea2253 + - 69f93450c57d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_paired @@ -1464,28 +1469,52 @@ tools: - 9b520009db81 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu +- name: bamtools_split_mapped + owner: iuc + revisions: + - 6dbef7ea2253 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_tag owner: iuc revisions: - e30af4e78cd3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: samtools_calmd +- name: pileup_interval owner: devteam revisions: - - 92ec40abcdcf + - 9c1c0b947e46 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: samtools_phase +- name: pileup_parser owner: devteam revisions: - - 1e5880498f52 + - 85bedbea8a12 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: bamhash - owner: bgruening +- name: sam2interval + owner: devteam revisions: - - 63f6f42d112b + - 75557c0908a9 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: tag_pileup_frequency + owner: iuc + revisions: + - 580e8bcb6413 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bamtools_split + owner: devteam + revisions: + - 96c9315b0e29 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bamtools_filter + owner: devteam + revisions: + - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamutil_diff @@ -1509,11 +1538,12 @@ tools: - name: bedtools owner: iuc revisions: - - 589e7e57fd6d - - dde39ba9c031 - - 07e8b80f278c - b8348686a0b9 - ce3c7f062223 + - 07e8b80f278c + - dde39ba9c031 + - 589e7e57fd6d + - a1a923cd89e8 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter @@ -1714,18 +1744,6 @@ tools: - ec699520444c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu -- name: flair_correct - owner: iuc - revisions: - - c784170f3b5e - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu -- name: flair_collapse - owner: iuc - revisions: - - 1fdcbfcca71c - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu - name: ngmlr owner: iuc revisions: @@ -1759,31 +1777,7 @@ tools: - name: nanoplot owner: iuc revisions: - - a3c4fe6f49ab - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu -- name: ont_fast5_api_multi_to_single_fast5 - owner: iuc - revisions: - - f98c015cebd8 - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu -- name: ont_fast5_api_single_to_multi_fast5 - owner: iuc - revisions: - - 435344af6dc9 - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu -- name: ont_fast5_api_compress_fast5 - owner: iuc - revisions: - - 82c6009bc120 - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu -- name: ont_fast5_api_fast5_subset - owner: iuc - revisions: - - 0defe443ea04 + - 0f1c34698076 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya @@ -1828,12 +1822,6 @@ tools: - ad011fc670d6 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu -- name: porechop - owner: iuc - revisions: - - 543cbeef3949 - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_times owner: iuc revisions: @@ -1912,6 +1900,48 @@ tools: - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu +- name: flair_correct + owner: iuc + revisions: + - c784170f3b5e + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: flair_collapse + owner: iuc + revisions: + - 1fdcbfcca71c + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ont_fast5_api_multi_to_single_fast5 + owner: iuc + revisions: + - f98c015cebd8 + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ont_fast5_api_single_to_multi_fast5 + owner: iuc + revisions: + - 435344af6dc9 + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ont_fast5_api_compress_fast5 + owner: iuc + revisions: + - 82c6009bc120 + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ont_fast5_api_fast5_subset + owner: iuc + revisions: + - 0defe443ea04 + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: porechop + owner: iuc + revisions: + - 543cbeef3949 + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc owner: iuc revisions: @@ -1924,10 +1954,16 @@ tools: - 63e02ef6e153 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu -- name: annotation_profiler +- name: concat owner: devteam revisions: - - 3b33da018e74 + - 73ca13a7ec5f + tool_panel_section_label: Operate on Genomic Intervals + tool_shed_url: toolshed.g2.bx.psu.edu +- name: join + owner: devteam + revisions: + - 718d04143c31 tool_panel_section_label: Operate on Genomic Intervals tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -1942,22 +1978,16 @@ tools: - 038ecf54cbec tool_panel_section_label: Operate on Genomic Intervals tool_shed_url: toolshed.g2.bx.psu.edu -- name: concat - owner: devteam +- name: translate_bed_sequences + owner: jjohnson revisions: - - 73ca13a7ec5f + - d328db400280 tool_panel_section_label: Operate on Genomic Intervals tool_shed_url: toolshed.g2.bx.psu.edu -- name: join +- name: annotation_profiler owner: devteam revisions: - - 718d04143c31 - tool_panel_section_label: Operate on Genomic Intervals - tool_shed_url: toolshed.g2.bx.psu.edu -- name: translate_bed_sequences - owner: jjohnson - revisions: - - d328db400280 + - 3b33da018e74 tool_panel_section_label: Operate on Genomic Intervals tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_bed_on_splice_junctions @@ -1966,22 +1996,22 @@ tools: - 915e5c5e02e6 tool_panel_section_label: Operate on Genomic Intervals tool_shed_url: toolshed.g2.bx.psu.edu -- name: extract_genomic_dna +- name: length_and_gc_content owner: iuc revisions: - - 5cc8e93ee98f + - f088370d2a3c tool_panel_section_label: Fetch Sequences / Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: length_and_gc_content +- name: fraggenescan owner: iuc revisions: - - f088370d2a3c + - 2dfb2fba4081 tool_panel_section_label: Fetch Sequences / Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: fraggenescan +- name: extract_genomic_dna owner: iuc revisions: - - 2dfb2fba4081 + - 5cc8e93ee98f tool_panel_section_label: Fetch Sequences / Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_locate @@ -1990,28 +2020,22 @@ tools: - 642d73815dd1 tool_panel_section_label: Fetch Sequences / Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: gffcompare +- name: bakta owner: iuc revisions: - - f99dd58de04f - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: cpat - owner: bgruening - revisions: - - 8e9e228c54c4 + - 3f0aa1b3e816 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: goseq +- name: tbprofiler owner: iuc revisions: - - 602de62d995b + - 2c68b0c38785 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: busco +- name: annotatemyids owner: iuc revisions: - - bb935709506a + - 3e1f6f6d557e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: optitype @@ -2020,24 +2044,12 @@ tools: - fd974c5df8bc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: prokka - owner: crs4 - revisions: - - 8a22554cdde2 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - 91887494eb97 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: tbprofiler - owner: iuc - revisions: - - 45083d070fb8 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: hmmer_nhmmer owner: iuc revisions: @@ -2080,24 +2092,12 @@ tools: - d753d9169482 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: kofamscan - owner: iuc - revisions: - - 23494763e39e - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 owner: iuc revisions: - 4a7f4b0cc0a3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: annotatemyids - owner: iuc - revisions: - - fe3ca740a485 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite owner: nml revisions: @@ -2119,7 +2119,7 @@ tools: - name: mitos owner: iuc revisions: - - f20804c311de + - c7553ba39670 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -2146,22 +2146,16 @@ tools: - 31812e7a1315 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: bp_genbank2gff3 - owner: iuc - revisions: - - 11c3eb512633 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 624606f7c996 + - 033755194fe9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: seq2hla owner: iuc revisions: - - 5a7cd6c39085 + - 86d0ce0560a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: fastani @@ -2170,36 +2164,6 @@ tools: - 2c7ac12ad75a tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: transit_tn5gaps - owner: iuc - revisions: - - 3f5fc4b09496 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: transit_resampling - owner: iuc - revisions: - - 885459e1c83b - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: transit_hmm - owner: iuc - revisions: - - 7db455b6434b - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: transit_gumbel - owner: iuc - revisions: - - 8fc50fe60127 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: tetyper - owner: iuc - revisions: - - edcf603bedfd - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: @@ -2212,22 +2176,22 @@ tools: - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: fargene +- name: kobas owner: iuc revisions: - - 239ce9f24386 + - 20f1b45dea63 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: kobas +- name: tbvcfreport owner: iuc revisions: - - 20f1b45dea63 + - 4934c0ac6197 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: gff_to_prot +- name: tb_variant_filter owner: iuc revisions: - - 07d7991bf205 + - ee4a90760848 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: gprofiler_snpense @@ -2242,10 +2206,10 @@ tools: - 7d18814397a7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: gprofiler_gost +- name: gff_to_prot owner: iuc revisions: - - bf39cdd007f5 + - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: gprofiler_orth @@ -2260,40 +2224,28 @@ tools: - 8ee097f1763d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: abricate - owner: iuc - revisions: - - c2ef298da409 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: blastxml_to_gapped_gff3 owner: iuc revisions: - 561e827baa5f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: maker +- name: goseq owner: iuc revisions: - - 370c210d9541 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: column_maker - owner: devteam - revisions: - - 9cd341095afd + - 602de62d995b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: socru +- name: snap_training owner: iuc revisions: - - ce0c9fe32e04 + - 2a598c0aa042 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: snap_training +- name: fgsea owner: iuc revisions: - - 2a598c0aa042 + - 17eb1e0d711f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker_map_ids @@ -2302,22 +2254,22 @@ tools: - e906fa778440 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: fgsea +- name: homer_scanmotifgenomewide owner: iuc revisions: - - 17eb1e0d711f + - f15794662a69 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: sortmerna - owner: rnateam +- name: homer_findmotifsgenome + owner: iuc revisions: - - eb35257d2e29 + - 081139509124 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: spaln +- name: homer_gtf_to_annotations owner: iuc revisions: - - 2e92e1929cb1 + - df55927535ed tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -2332,22 +2284,16 @@ tools: - 2c7c9646ccf0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: jcvi_gff_stats - owner: iuc - revisions: - - 8cffbd184762 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: hammock owner: hammock revisions: - 4db310b7e37c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: integron_finder +- name: picrust_metagenome_contributions owner: iuc revisions: - - 1ae00120dd24 + - bc71c2b53097 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tmhmm_and_signalp @@ -2356,30 +2302,6 @@ tools: - e1996f0f4e85 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: bakta - owner: iuc - revisions: - - da5f1924bb2e - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: pfamscan - owner: bgruening - revisions: - - 15cff34c2005 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: gecco - owner: althonos - revisions: - - cc91d730cc4f - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: picrust_metagenome_contributions - owner: iuc - revisions: - - bc71c2b53097 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table owner: iuc revisions: @@ -2416,23 +2338,16 @@ tools: - 012171ba9fce tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: segmentation_fold - owner: yhoogstrate - revisions: - - 09e921a25c68 - - 4d16cf9414cf - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: gubbins owner: iuc revisions: - 96e6283e4745 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: probmetab - owner: mmonsoor +- name: sortmerna + owner: rnateam revisions: - - 3a9914b37f2f + - eb35257d2e29 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: lcmsmatching @@ -2441,36 +2356,12 @@ tools: - 253d531a0193 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: nucleosome_prediction - owner: bgruening - revisions: - - 2c42bb973ac3 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups owner: iuc revisions: - 3b974afde673 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: miranda - owner: tgac - revisions: - - bf6976462251 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: dotknot - owner: bgruening - revisions: - - 42d20ff5da1b - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: blast2go - owner: peterjc - revisions: - - 8664c4c94764 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: hmmer_alimask owner: iuc revisions: @@ -2501,29 +2392,34 @@ tools: - a28fd001de59 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: find_subsequences - owner: bgruening - revisions: - - d882a0a75759 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: gotohscan owner: rnateam revisions: - 6845ddcd5588 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: cryptogenotyper - owner: nml +- name: busco + owner: iuc revisions: - - d4a96287909e + - 94170eee0ad8 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: dgidb_annotator - owner: devteam +- name: prokka + owner: crs4 revisions: - - c5bb987015c5 - - 792f3cb0eff4 + - 8a22554cdde2 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: homer_findmotifs + owner: iuc + revisions: + - 453ebddf5bb2 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: kofamscan + owner: iuc + revisions: + - 23494763e39e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: hhsearch @@ -2550,22 +2446,22 @@ tools: - 73c58e2debd0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: tbvcfreport +- name: bp_genbank2gff3 owner: iuc revisions: - - 4934c0ac6197 + - 11c3eb512633 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: tb_variant_filter +- name: transit_tn5gaps owner: iuc revisions: - - ee4a90760848 + - 3f5fc4b09496 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: lorikeet_spoligotype +- name: transit_resampling owner: iuc revisions: - - f9c37d0b3002 + - 885459e1c83b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: spotyping @@ -2577,91 +2473,97 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 1e10310ce195 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: repeat_masker - owner: bgruening +- name: transit_hmm + owner: iuc revisions: - - 3f987772e283 + - 7db455b6434b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: homer_scanmotifgenomewide +- name: transit_gumbel owner: iuc revisions: - - db456c398880 + - 8fc50fe60127 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: homer_annotatepeaks +- name: tetyper owner: iuc revisions: - - 35dc2f57d755 + - edcf603bedfd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: homer_findmotifsgenome +- name: funannotate_clean owner: iuc revisions: - - a8f207b43f64 + - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: homer_gtf_to_annotations +- name: funannotate_sort owner: iuc revisions: - - 396cf2c12173 + - 52af33194019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: hamronize_tool +- name: funannotate_predict owner: iuc revisions: - - 41c7e03b3eab + - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: hamronize_summarize +- name: funannotate_compare owner: iuc revisions: - - 243c87f34f39 + - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: funannotate_clean +- name: funannotate_annotate owner: iuc revisions: - - a230ea445788 + - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: funannotate_sort +- name: fargene owner: iuc revisions: - - b3cf4684e9c7 + - 239ce9f24386 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: interproscan + owner: bgruening + revisions: + - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: funannotate_predict +- name: maker owner: iuc revisions: - - 2bba2ff070d9 + - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: funannotate_compare +- name: gprofiler_gost owner: iuc revisions: - - 563a19373357 + - bf39cdd007f5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: funannotate_annotate +- name: abricate owner: iuc revisions: - - 14f588312c56 + - c2ef298da409 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: interproscan - owner: bgruening +- name: column_maker + owner: devteam revisions: - - 74810db257cc + - 9cd341095afd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: legsta +- name: isescan owner: iuc revisions: - - 579f1cabfe79 + - 19f42b3ea391 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: te_finder @@ -2670,34 +2572,168 @@ tools: - 2edb80d68a1b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: isescan +- name: plasmidfinder owner: iuc revisions: - - 19f42b3ea391 + - 7075b7a5441b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: miniprot +- name: socru owner: iuc revisions: - - ce04c239454b + - ce0c9fe32e04 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: netboxr +- name: edta owner: bgruening revisions: - - 785ed8621503 + - f1a157358d4d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: plasmidfinder +- name: gffcompare + owner: iuc + revisions: + - f99dd58de04f + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: pfamscan + owner: bgruening + revisions: + - 15cff34c2005 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: pharokka + owner: iuc + revisions: + - f05c3732764a + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: spaln + owner: iuc + revisions: + - 2e92e1929cb1 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: jcvi_gff_stats + owner: iuc + revisions: + - 8cffbd184762 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: multigsea + owner: iuc + revisions: + - 28e29a3d0eda + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: segmentation_fold + owner: yhoogstrate + revisions: + - 4d16cf9414cf + - 09e921a25c68 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: probmetab + owner: mmonsoor + revisions: + - 3a9914b37f2f + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: nucleosome_prediction + owner: bgruening + revisions: + - 2c42bb973ac3 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: miranda + owner: tgac + revisions: + - bf6976462251 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: dotknot + owner: bgruening + revisions: + - 42d20ff5da1b + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: find_subsequences + owner: bgruening + revisions: + - d882a0a75759 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cryptogenotyper + owner: nml + revisions: + - d4a96287909e + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: dgidb_annotator + owner: devteam + revisions: + - 792f3cb0eff4 + - c5bb987015c5 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: lorikeet_spoligotype + owner: iuc + revisions: + - f9c37d0b3002 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: repeat_masker + owner: bgruening + revisions: + - ba6d2c32f797 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: homer_annotatepeaks + owner: iuc + revisions: + - dcd291aeb8a9 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: hamronize_tool + owner: iuc + revisions: + - 41c7e03b3eab + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: hamronize_summarize + owner: iuc + revisions: + - 243c87f34f39 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: gecco + owner: althonos + revisions: + - cc91d730cc4f + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: legsta + owner: iuc + revisions: + - 579f1cabfe79 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: miniprot owner: iuc revisions: - - e23b96d79dc0 + - 52bdc302299b + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: netboxr + owner: bgruening + revisions: + - 785ed8621503 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: miniprot_index owner: iuc revisions: - - d6a874226260 + - 3ccb407501d8 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -2706,10 +2742,22 @@ tools: - 18a46265455b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: edta +- name: integron_finder + owner: iuc + revisions: + - 4768f7f8e93f + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpat owner: bgruening revisions: - - f1a157358d4d + - 8e9e228c54c4 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: braker + owner: genouest + revisions: + - ca7c12566894 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -2730,46 +2778,52 @@ tools: - 5efbd15675ca tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: chromeister +- name: mummer_dnadiff owner: iuc revisions: - - b768cc4cca40 + - c9685bc0407c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: maf_stats +- name: mummer_nucmer owner: iuc revisions: - - 0c84cce7b030 + - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: mummer_mummer +- name: mummer_delta_filter owner: iuc revisions: - - bcd65de9725b + - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: mummer_mummerplot - owner: iuc +- name: hammock + owner: hammock revisions: - - 4fc0cb2ac8ae + - afddbcbc8ee8 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: mummer_delta_filter - owner: iuc +- name: muscle + owner: crs4 revisions: - - fbca557a4847 + - 533b3b2a1e66 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: mummer_nucmer +- name: mafft + owner: rnateam + revisions: + - a65296ffb4a0 + tool_panel_section_label: Multiple Alignments + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cd_hit owner: iuc revisions: - - e18267f90096 + - 7807800a3d03 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: mummer_dnadiff +- name: mummer_mummer owner: iuc revisions: - - c9685bc0407c + - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords @@ -2778,12 +2832,30 @@ tools: - b4124df98b26 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu +- name: mummer_mummerplot + owner: iuc + revisions: + - 4fc0cb2ac8ae + tool_panel_section_label: Multiple Alignments + tool_shed_url: toolshed.g2.bx.psu.edu - name: kc_align owner: iuc revisions: - 97476dfde728 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu +- name: chromeister + owner: iuc + revisions: + - b768cc4cca40 + tool_panel_section_label: Multiple Alignments + tool_shed_url: toolshed.g2.bx.psu.edu +- name: maf_stats + owner: iuc + revisions: + - 0c84cce7b030 + tool_panel_section_label: Multiple Alignments + tool_shed_url: toolshed.g2.bx.psu.edu - name: pipelign owner: iuc revisions: @@ -2802,156 +2874,24 @@ tools: - 99f8b4e631e5 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: hammock - owner: hammock - revisions: - - afddbcbc8ee8 - tool_panel_section_label: Multiple Alignments - tool_shed_url: toolshed.g2.bx.psu.edu - name: format_cd_hit_output owner: bebatut revisions: - 4015e9d6d277 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: muscle - owner: crs4 - revisions: - - 533b3b2a1e66 - tool_panel_section_label: Multiple Alignments - tool_shed_url: toolshed.g2.bx.psu.edu - name: compalignp owner: rnateam revisions: - 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toolshed.g2.bx.psu.edu -- name: minia - owner: iuc - revisions: - - 734cd5f1c1b2 - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu - name: flye owner: bgruening revisions: - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: quast - owner: iuc - revisions: - - 3061c8b029e5 - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu - name: miniasm owner: iuc revisions: @@ -3027,13 +2937,7 @@ tools: - name: abyss owner: iuc revisions: - - 8f1b150a2487 - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: unicycler - owner: iuc - revisions: - - d10bdad2fd17 + - 7547fcab5d19 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: idba_ud @@ -3048,6 +2952,12 @@ tools: - 5c5806e23338 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu +- name: unicycler + owner: iuc + revisions: + - d10bdad2fd17 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: @@ -3078,10 +2988,10 @@ tools: - fd128c111ab0 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: disco +- name: quast owner: iuc revisions: - - dfefaf2bab95 + - 72472698a2df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades @@ -3090,12 +3000,6 @@ tools: - 1d06c8b38e77 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: meryl - owner: iuc - revisions: - - 29dabd8db6f2 - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu - name: mira_assembler owner: peterjc revisions: @@ -3120,10 +3024,10 @@ tools: - f20db7280f89 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: crispr_recognition_tool +- name: hifiasm owner: bgruening revisions: - - db0f5c1cb227 + - 71740308d412 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minced @@ -3132,148 +3036,215 @@ tools: - e8cbdbc4de58 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: merqury +- name: trycycler_cluster owner: iuc revisions: - - f8113c25bc6b + - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: genomescope +- name: trycycler_consensus owner: iuc revisions: - - 01210c4e9144 + - 19bdfd1e6fe3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: pretext_map +- name: trycycler_partition owner: iuc revisions: - - dfb8a4497339 + - 80a17897564d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: bellerophon +- name: trycycler_reconcile_msa owner: iuc revisions: - - 25ca5d73aedf + - cb1e3db43020 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: mitohifi - owner: bgruening +- name: genomescope + owner: iuc revisions: - - f6065bc6e428 + - 01210c4e9144 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: raven +- name: trycycler_subsample owner: iuc revisions: - - 2b2a352488fa + - 2628f6790eda tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: ragtag +- name: mitobim owner: iuc revisions: - - b3c3217c0cbc + - ea46115c7f1e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: tgsgapcloser - owner: bgruening +- name: trimns + owner: iuc revisions: - - 86fa46d3ce2e + - 30178a68af68 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: hypo +- name: purge_dups owner: iuc revisions: - - d7c48cf1bf50 + - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: spades_rnaviralspades +- name: aegean_parseval owner: iuc revisions: - - d5fb354f745d + - 1b52f0c8ad7f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: cactus_cactus - owner: galaxy-australia +- name: aegean_locuspocus + owner: iuc 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tool_shed_url: toolshed.g2.bx.psu.edu -- name: links +- name: minia owner: iuc revisions: - - 7acd9ade2dd1 + - 734cd5f1c1b2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: gfastats - owner: bgruening +- name: raven + owner: iuc revisions: - - 5799092ffdff + - 2b2a352488fa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: yahs +- name: ragtag owner: iuc revisions: - - 39495e107274 + - b3c3217c0cbc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: velvet - owner: devteam +- name: merqury + owner: iuc revisions: - - 920677cd220f + - f8113c25bc6b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: cap3 - owner: artbio +- name: tgsgapcloser + owner: bgruening revisions: - - d76a0d8a9eac + - 86fa46d3ce2e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: smudgeplot - owner: galaxy-australia +- name: hypo + owner: iuc revisions: - - 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+- name: bionano_scaffold + owner: bgruening + revisions: + - 3371c5bdc17a + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bellerophon + owner: iuc + revisions: + - 25ca5d73aedf + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: links + owner: iuc + revisions: + - 7acd9ade2dd1 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: mitohifi + owner: bgruening + revisions: + - 99ddbf037d98 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: gfastats + owner: bgruening + revisions: + - 5799092ffdff + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: smudgeplot + owner: galaxy-australia + revisions: + - 5a0ddb4dc3a4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 8b330a577046 + - 06bcf65179fb + - 611219887a48 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minipolish @@ -3282,6 +3253,18 @@ tools: - 1f9f2edc8cf4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu +- name: cactus_cactus + owner: galaxy-australia + revisions: + - 9eeb13a92d79 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cactus_export + owner: galaxy-australia + revisions: + - d7ce0ec78e51 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu - name: instagraal owner: bgruening revisions: @@ -3294,41 +3277,106 @@ tools: - 6ee7eb5821f0 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu +- name: spades_rnaviralspades + owner: iuc + revisions: + - d5fb354f745d + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: spades_metaviralspades + owner: iuc + revisions: + - 328aa71f0f3c + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: nextdenovo + owner: bgruening + 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owner: devteam +- name: verkko + owner: iuc revisions: - - ecc974513241 + - cf54dafa0403 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bwa_mem2 + owner: iuc + revisions: + - bfaa0d22c2e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: lastz +- name: lastz_paired_reads owner: devteam revisions: - - 3e1ea2facca6 + - ecc974513241 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -3337,48 +3385,84 @@ tools: - b46e7d48076a tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: minimap2 +- name: hisat2 owner: iuc revisions: - - 11a0d50a54e6 + - f4af63aaf57a tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: hisat2 +- name: kma owner: iuc revisions: - - f4af63aaf57a + - 95ab864b281a tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: rna_starsolo - owner: iuc +- name: bismark + owner: 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name: megablast_wrapper + owner: devteam + revisions: + - fb2e0e1dac89 + tool_panel_section_label: Mapping + tool_shed_url: toolshed.g2.bx.psu.edu +- name: lastz + owner: devteam + revisions: + - 37b497aa133f + tool_panel_section_label: Mapping + tool_shed_url: toolshed.g2.bx.psu.edu +- name: minimap2 owner: iuc revisions: - - 95ab864b281a + - be1d967337e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: star_fusion +- name: rna_starsolo owner: iuc revisions: - - 137942fac417 + - 13022c3d3076 + tool_panel_section_label: Mapping + tool_shed_url: toolshed.g2.bx.psu.edu +- name: rgrnastar + owner: iuc + revisions: + - 3ea5a2a63fa2 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie2 @@ -3387,10 +3471,10 @@ tools: - 03e9b2fbc005 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: segemehl - owner: rnateam +- name: bbtools_bbmap + owner: iuc revisions: - - 9c0d4ec99ba9 + - 517464809c33 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: graphmap_overlap @@ -3405,12 +3489,6 @@ tools: - 190175f4e143 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: tophat2 - owner: devteam - revisions: - - 16c4255042be - tool_panel_section_label: Mapping - tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_color_wrappers owner: devteam revisions: @@ -3429,124 +3507,34 @@ tools: - a07a2d9ddd42 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: bwa_mem2 +- name: smgu_frameshift_deletions_checks owner: iuc revisions: - - b4a22d90cce9 - tool_panel_section_label: Mapping + - e8971ca74398 + tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bbtools_bbmap +- name: vardict_java owner: iuc revisions: - - 858a65b52cf9 - tool_panel_section_label: Mapping + - e0734e88a104 + tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: ucsc_fatovcf +- name: vg_view owner: iuc revisions: - - 78df8fc2b3ab + - ee62774bb5bd tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_stats +- name: vg_deconstruct owner: iuc revisions: - - a2f8dc22d7c0 + - 76d18b1e970b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_roh - owner: iuc - revisions: - - bdc67eeb0bc9 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_reheader - owner: iuc - revisions: - - 8057cf55fa41 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_query - owner: iuc - revisions: - - a850902cac64 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_plugin_setgt - owner: iuc - revisions: - - 262bba5b90ef - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_plugin_frameshifts - owner: iuc - revisions: - - 399b40b2bcab - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_filter - owner: iuc - revisions: - - 656a916779fe - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_csq - owner: iuc - revisions: - - f01b2c9506b9 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_convert_to_vcf - owner: iuc - revisions: - - 4935320a59a8 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_convert_from_vcf - owner: iuc - revisions: - - cacc9970727a - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_annotate - owner: iuc - revisions: - - 3f62d4939d54 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_call - owner: iuc - revisions: - - f0d44631365f - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_consensus - owner: iuc - revisions: - - 147de996e34f - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: varscan_somatic - owner: iuc - revisions: - - cf8ffc79db67 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: naive_variant_caller - owner: blankenberg - revisions: - - aff38ea879f1 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: varscan_version_2 - owner: devteam - revisions: - - bc1e0cd41241 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: varscan_copynumber +- name: vg_convert owner: iuc revisions: - - 9f8dbbbc0267 + - 7366704232b6 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: strelka_germline @@ -3555,58 +3543,16 @@ tools: - 19481653a22f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: sansa_annotate - owner: iuc - revisions: - - 30079fa4e2fd - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: strelka_somatic - owner: iuc - revisions: - - edbdbc64b397 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: varscan_mpileup - owner: iuc - revisions: - - db94eadb92c1 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: delly_filter - owner: iuc - revisions: - - 74f9f312c713 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: delly_merge - owner: iuc - revisions: - - 6c44bbc0eaa5 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: delly_call - owner: iuc - revisions: - - c34eab9d5134 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: delly_lr - owner: iuc - revisions: - - 97f649646cc1 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu - name: delly_classify owner: iuc revisions: - df4300f300e4 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: delly_cnv +- name: strelka_somatic owner: iuc revisions: - - 8ad49c4272ea + - edbdbc64b397 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfanno @@ -3627,31 +3573,16 @@ tools: - b4b6b660293a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpfreqplot - owner: iuc - revisions: - - 3d0adeee3f2b - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: variant_analyzer - owner: iuc - revisions: - - 3f1dbd2c59bf - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpsift +- name: lumpy_sv owner: iuc revisions: - - b04635ebfab0 - - 5fab4f81391d - - 2b3e65a4252f - - 09d6806c609e + - 88b35d91a662 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: lumpy_sv +- name: bcftools_consensus owner: iuc revisions: - - 88b35d91a662 + - 147de996e34f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lumpy_prep @@ -3678,12 +3609,6 @@ tools: - 16d22eee0fe3 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: artic_minion - owner: iuc - revisions: - - 6f52ebc01098 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu - name: cutesv owner: iuc revisions: @@ -3696,24 +3621,6 @@ tools: - 93c4b04a0769 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: vardict_java - owner: iuc - revisions: - - e0734e88a104 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: control_freec - owner: iuc - revisions: - - f923c54a17ee - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: gatk4_mutect2 - owner: iuc - revisions: - - 53ce8be43212 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat owner: iuc revisions: @@ -3744,12 +3651,6 @@ tools: - 971e07ca4456 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: seqwish - owner: iuc - revisions: - - 0c415ba215e7 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu - name: odgi_viz owner: iuc revisions: @@ -3762,24 +3663,6 @@ tools: - 6584dfcc7165 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: vg_view - owner: iuc - revisions: - - ee62774bb5bd - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: vg_deconstruct - owner: iuc - revisions: - - 76d18b1e970b - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: vg_convert - owner: iuc - revisions: - - 7366704232b6 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: @@ -3924,40 +3807,40 @@ tools: - 6ea73d6151ec tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_norm +- name: bcftools_call owner: iuc revisions: - - ebb2e12a6de1 + - f0d44631365f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_plugin_color_chrs +- name: bcftools_norm owner: iuc revisions: - - 36960e552ddc + - ebb2e12a6de1 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_cnv +- name: bcftools_csq owner: iuc revisions: - - 6d35a3780bfd + - f01b2c9506b9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snp_dists +- name: bcftools_plugin_frameshifts owner: iuc revisions: - - 1959cc43b414 + - 399b40b2bcab tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: tag_pileup_frequency +- name: bcftools_plugin_color_chrs owner: iuc revisions: - - 6432735cdb22 + - 36960e552ddc tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snp_sites +- name: bcftools_cnv owner: iuc revisions: - - 5804f786060d + - 6d35a3780bfd tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: exomedepth @@ -3972,626 +3855,730 @@ tools: - a5937157062f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpeff +- name: varscan_somatic owner: iuc revisions: - - e8adfc4c0a6b - - 5c7b70713fb5 - - 5b80f544c67f + - cf8ffc79db67 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: basil +- name: bcftools owner: iuc revisions: - - e6ef29001647 + - bdd0cb7fbedf tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_gtcheck +- name: snpsift owner: iuc revisions: - - 3eac729e66c9 + - 5fab4f81391d + - 09d6806c609e + - 2b3e65a4252f + - b04635ebfab0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_isec +- name: vt_variant_tools owner: iuc revisions: - - 63aabc920911 + - 6e073fc99d9c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_mpileup +- name: varscan_copynumber owner: iuc revisions: - - 03191140c66a + - 9f8dbbbc0267 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_plugin_split_vep +- name: sansa_annotate owner: iuc revisions: - - d55feecb6dc1 + - b1ca9fce4749 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_view - owner: iuc +- name: varscan_version_2 + owner: devteam revisions: - - abc3ced31cd1 + - bc1e0cd41241 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools +- name: varscan_mpileup owner: iuc revisions: 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toolshed.g2.bx.psu.edu -- name: king +- name: variant_analyzer owner: iuc revisions: - - 1932808c6fab + - 3f1dbd2c59bf tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: artic_guppyplex +- name: bcftools_roh owner: iuc revisions: - - 372def2f8fd6 + - bdc67eeb0bc9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: pharmcat - owner: bgruening +- name: bcftools_reheader + owner: iuc revisions: - - 891283e0ee89 + - 8057cf55fa41 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bbtools_callvariants +- name: bcftools_query owner: iuc revisions: - - d1912018a603 + - a850902cac64 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: ensembl_vep +- name: bcftools_isec owner: iuc revisions: - - b43df0ce6c87 + - 63aabc920911 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: breseq +- name: bcftools_gtcheck 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tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: picrust2_pathway_pipeline + owner: iuc + revisions: + - 6077821e8ae7 + tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: picrust2_pipeline owner: iuc revisions: - - ea30d3089354 + - 540aedfc81c7 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu -- name: gstf_preparation - owner: earlhaminst +- name: picrust2_place_seqs + owner: iuc revisions: - - 9c62ad7dd113 + - 680fb3eb574c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu -- name: phyml +- name: picrust2_shuffle_predictions owner: iuc revisions: - - 2bf47d57ebb5 + - 881f2faa5fe7 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: sarscov2summary @@ -5313,8 +5575,8 @@ tools: - name: ete owner: earlhaminst revisions: - - 276e3ee68c37 - ed74587a13c8 + - 276e3ee68c37 - 2db72467da51 tool_panel_section_label: Phylogenetics 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+- name: scater_plot_dist_scatter owner: iuc revisions: - - 99f912d5af9f + - ef4c80837bc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca @@ -5565,34 +5827,40 @@ tools: - c99ba278dfa9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu -- name: scater_plot_exprs_freq - owner: iuc +- name: music_inspect_eset + owner: bgruening revisions: - - 058b40656107 + - 7705cc75ac18 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu -- name: scater_plot_dist_scatter +- name: music_compare + owner: bgruening + revisions: + - 4447ed460308 + tool_panel_section_label: Single-cell + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cite_seq_count owner: iuc revisions: - - ef4c80837bc5 + - 3df3d1b51110 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu -- name: scater_normalize +- name: episcanpy_build_matrix owner: iuc revisions: - - 946179ef029c + - 31a21ba2c5ea tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu -- name: scater_filter +- name: episcanpy_preprocess owner: iuc revisions: - - 652923ce664f + - 29f5f25b9935 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu -- name: scater_create_qcmetric_ready_sce +- name: episcanpy_cluster_embed owner: iuc revisions: - - 8f333f90d8d6 + - f4713992f23a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -5625,40 +5893,34 @@ tools: - a6821f856a1e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu -- name: music_deconvolution - owner: bgruening - revisions: - - 2ba99a52bd44 - tool_panel_section_label: Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: music_construct_eset +- name: music_manipulate_eset owner: bgruening revisions: - - 282819d09a4f + - 22232092be53 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu -- name: 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toolshed.g2.bx.psu.edu -- name: qiime2__feature_table__filter_features_conditionally +- name: qiime2__phylogeny__raxml owner: q2d2 revisions: - - dbeb5a365844 + - 1f553c9cc99e tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__feature_table__heatmap +- name: qiime2__phylogeny__raxml_rapid_bootstrap owner: q2d2 revisions: - - a8de96a8b8eb + - 444a88ecf0d8 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__feature_table__merge_seqs +- name: qiime2__phylogeny__robinson_foulds owner: q2d2 revisions: - - b46e5d243a98 + - abe6db32295f tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__feature_table__summarize +- name: qiime2__quality_control__bowtie2_build owner: q2d2 revisions: - - c7553080ec2e + - dc6b98098f4f tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__feature_table__relative_frequency +- name: 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toolshed.g2.bx.psu.edu -- name: qiime2__phylogeny__raxml_rapid_bootstrap +- name: qiime2__sample_classifier__scatterplot owner: q2d2 revisions: - - 444a88ecf0d8 + - b2a04cea7140 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__phylogeny__robinson_foulds +- name: qiime2__sample_classifier__split_table owner: q2d2 revisions: - - abe6db32295f + - b3fdc6dd0eab tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__phylogeny__align_to_tree_mafft_raxml +- name: qiime2__sample_classifier__summarize owner: q2d2 revisions: - - c1018e6b9e55 + - 8fa73ff177a2 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__quality_control__evaluate_composition +- name: qiime2__taxa__barplot owner: q2d2 revisions: - - 8f17025fb019 + - 5750bac5b744 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__quality_control__evaluate_taxonomy +- name: qiime2__taxa__collapse owner: q2d2 revisions: - - 2719c0bf3bd7 + - 96d3a6a511bc tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__quality_control__exclude_seqs +- name: qiime2__taxa__filter_seqs owner: q2d2 revisions: - - f697a0b6a702 + - c4e992863672 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__sample_classifier__classify_samples +- name: qiime2__taxa__filter_table owner: q2d2 revisions: - - e5daff8f4e9e + - 4d6cd6706bfd tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__sample_classifier__classify_samples_ncv +- name: qiime2__vsearch__cluster_features_closed_reference owner: q2d2 revisions: - - 9c6128727a71 + - bdfd1704be32 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__sample_classifier__heatmap +- name: qiime2__vsearch__cluster_features_de_novo owner: q2d2 revisions: - - c8a9c7b66934 + - a753a1136636 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__sample_classifier__scatterplot +- name: qiime2__vsearch__cluster_features_open_reference owner: q2d2 revisions: - - b2a04cea7140 + - df39d339740c tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__taxa__collapse +- name: qiime2__vsearch__dereplicate_sequences owner: q2d2 revisions: - - 96d3a6a511bc + - 89cf98a14b38 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__taxa__filter_seqs +- name: qiime2__vsearch__fastq_stats owner: q2d2 revisions: - - c4e992863672 + - 826f1e13fbd1 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__vsearch__cluster_features_closed_reference +- name: qiime2__vsearch__merge_pairs owner: q2d2 revisions: - - bdfd1704be32 + - b26cb5419c39 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__vsearch__cluster_features_open_reference +- name: qiime2__vsearch__uchime_denovo owner: q2d2 revisions: - - df39d339740c + - a02a20641fb6 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__vsearch__merge_pairs +- name: qiime2__vsearch__uchime_ref owner: q2d2 revisions: - - b26cb5419c39 + - 7baf77299428 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__vsearch__dereplicate_sequences +- name: qiime2_core__tools__export owner: q2d2 revisions: - - 89cf98a14b38 + - d3b1853c4efd tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu - name: qiime2_core__tools__import @@ -14707,9 +15084,51 @@ tools: - 5d9a36073ed6 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__alignment__mafft_add +- name: qiime2__deblur__denoise_16s owner: q2d2 revisions: - - 4fde174f0118 + - 2572fc0f88f2 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu +- name: t2t_report + owner: devteam + revisions: + - 592acb9505fc + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: t2ps + owner: devteam + revisions: + - 4d9910e996f7 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: poisson2test + owner: devteam + revisions: + - 5ff18ec88181 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: lca_wrapper + owner: devteam + revisions: + - 33e8ed5a4601 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: gi2taxonomy + owner: devteam + revisions: + - 7b1b03c4465d + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: find_diag_hits + owner: devteam + revisions: + - acf51ff24c7d + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: count_covariates + owner: devteam + revisions: + - 14e304b70425 + tool_panel_section_label: GATK Tools + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/files/galaxy/config/tpv_rules_local.yml b/files/galaxy/config/tpv_rules_local.yml index a5758ba..6cd9715 100644 --- a/files/galaxy/config/tpv_rules_local.yml +++ b/files/galaxy/config/tpv_rules_local.yml @@ -30,6 +30,12 @@ tools: cores: int(job.get_param_values(app)['__job_resource']['cores']) params: walltime: "{int(job.get_param_values(app)['__job_resource']['time'])}" +# .*sra_tools.*: +# scheduling: +# require: +# - local_env +# reject: +# - pulsar # .*/bwa/.*: # scheduling: # require: @@ -38,6 +44,10 @@ tools: # scheduling: # require: # - pulsar + .*/alphafold/.*: + scheduling: + require: + - pulsar_gpu roles: training.*: @@ -54,6 +64,9 @@ destinations: max_accepted_cores: 1 params: tmp_dir: true + scheduling: + require: + - local_env singularity: runner: local_runner max_accepted_cores: 1 @@ -77,15 +90,78 @@ destinations: params: default_file_action: remote_transfer dependency_resolution: remote - jobs_directory: /storage/praha5-elixir/home/galaxyeu/pulsar-test/files/staging - persistence_directory: /storage/praha5-elixir/home/galaxyeu/pulsar-test/files/persisted_data + jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/staging" + persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/persistent" remote_metadata: false rewrite_parameters: true transport: curl outputs_to_working_directory: false + singularity_enabled: true + singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR" + container_resolvers: + - type: explicit_singularity + - type: mulled_singularity + env: + # Ensuring a consistent collation environment is good for reproducibility. + - name: LC_ALL + value: C + - name: TMPDIR + value: "$SCRATCHDIR" + - name: TMP + value: "$SCRATCHDIR" + - name: TEMP + value: "$SCRATCHDIR" + scheduling: + require: + - pulsar + pulsar_gpu: + runner: pulsar_gpu_runner + max_accepted_cores: 128 + max_accepted_mem: 512 + max_accepted_gpus: 2 + max_cores: 16 + max_mem: 64 + max_gpus: 1 + params: + default_file_action: remote_transfer + transport: curl + dependency_resolution: remote + jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/staging" + persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/persistent" + remote_metadata: false + rewrite_parameters: true + outputs_to_working_directory: false + singularity_enabled: true + singularity_run_extra_arguments: '--nv' + singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data/2.3:ro' + env: + # The cache directory holds the docker containers that get converted + - name: SINGULARITY_CACHEDIR + value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" + - name: APPTAINER_CACHEDIR + value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" + # Singularity uses a temporary directory to build the squashfs filesystem + - name: SINGULARITY_TMPDIR + value: "/storage/praha5-elixir/home/galaxyeu/singularity/tmp" + - name: APPTAINER_TMPDIR + value: "/storage/praha5-elixir/home/galaxyeu/singularity/tmp" + # Alphafold specific variables + - name: ALPHAFOLD_DB + value: "/storage/brno11-elixir/projects/alphafold/alphafold.db-2.3.1" + # Default variables + - name: TMPDIR + value: "$SCRATCHDIR" + - name: TMP + value: "$SCRATCHDIR" + - name: TEMP + value: "$SCRATCHDIR" + # Ensuring a consistent collation environment is good for reproducibility. + - name: LC_ALL + value: C scheduling: require: - pulsar + - gpu pulsar-training: inherits: pulsar runner: pulsar_runner diff --git a/files/galaxy/tools/testing.xml b/files/galaxy/tools/testing.xml index 6db2e85..3a5e766 100644 --- a/files/galaxy/tools/testing.xml +++ b/files/galaxy/tools/testing.xml @@ -1,12 +1,15 @@ - + - "$output1"]]> + - + + - + + diff --git a/files/galaxy/welcome.html b/files/galaxy/welcome.html index 5cb8978..3be12bc 100644 --- a/files/galaxy/welcome.html +++ b/files/galaxy/welcome.html @@ -1,19 +1,30 @@ - - - + + + -
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Výtejte na usegalaxy.cz!

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Tato služba je součástí e-infra.cz infrastruktury.

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Zatím mámskušebný provoz, jakékoliv problémy hlaste na regalaxy@rt.cesnet.cz

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Dear users, we are still in testing mode, so we kindly ask you to report any troubles at regalaxy@rt.cesnet.cz. So far, we know that a few tools are incompatible with the latest Galaxy version. Sometimes your jobs may end up in the Error state or even in the Complete state (but empty with 0 size) with messages like: =>> PBS: job killed:... That means the resources need to be fit to means of the tool, and reporting this fact will help us improve the service. On behalf of the admin group, thank you. -

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Welcome to UseGalaxy CZ

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This service is part of the e-infra.cz infrastructure and Elixir Czech Republic.

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Dear users, we are still in testing mode, so we kindly ask you to report any troubles at regalaxy@rt.cesnet.cz. So far, we know that a few tools are incompatible with the latest Galaxy version. Sometimes your jobs may end up in the Error state or even in the Complete state (but empty with 0 size) with messages like: =>> PBS: job killed:... That means the resources need to be fit to means of the tool, and reporting this fact will help us improve the service. On behalf of the admin group, thank you. +



diff --git a/galaxy.yml b/galaxy.yml index 3768316..1a91bfe 100644 --- a/galaxy.yml +++ b/galaxy.yml @@ -41,6 +41,27 @@ - git: repo: 'https://github.com/usegalaxy-eu/libraries-training-repo' dest: /libraries/ + - name: Create the RBD storage directory + file: + owner: galaxy + group: galaxy + path: /rbd/data + state: directory + mode: '0755' + - name: Create the nginx upload job files store + file: + owner: www-data + group: galaxy + path: /rbd/data/_upload_job_files + state: directory + mode: '0775' + - name: Create the client body temp path + file: + owner: www-data + group: galaxy + path: /rbd/data/nginx_upload_store + state: directory + mode: '0775' roles: - galaxyproject.tusd - usegalaxy_eu.apptainer diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index 6a50044..3869017 100644 --- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -7,10 +7,11 @@ galaxy_manage_cleanup: true galaxy_layout: root-dir galaxy_root: /srv/galaxy galaxy_user: {name: "{{ galaxy_user_name }}", shell: /bin/bash} -galaxy_commit_id: release_23.0 # 7a9ba0c6529d72517c7627422eac16eadff15b46 +galaxy_commit_id: 1ad49865fbeb03551cf7774dc0c12e5cd27ff797 # release_23.0 +#galaxy_commit_id: 72070dbd0a6d0f418d0b8f914825ea2b8e6a0a88 galaxy_force_checkout: true miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda" -miniconda_version: 4.12.0 +miniconda_version: 23.5.2 # 23.5.0 # 4.12.0 miniconda_channels: ['conda-forge', 'defaults'] # Galaxy Job Configuration @@ -22,7 +23,7 @@ galaxy_job_config: pulsar_runner: load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner galaxy_url: "https://{{ rabbitmq_hostname }}" - amqp_url: "pyamqp://galaxy:{{ rabbitmq_users_password.galaxy_gpu }}@{{ rabbitmq_hostname }}:5671/galaxy_gpu?ssl=1" + amqp_url: "pyamqp://pulsar:{{ rabbitmq_users_password.pulsar }}@{{ rabbitmq_hostname }}:5671/pulsar?ssl=1" amqp_acknowledge: true amqp_ack_republish_time: 1200 amqp_consumer_timeout: 2 @@ -32,13 +33,13 @@ galaxy_job_config: pulsar_gpu_runner: load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner galaxy_url: "https://{{ rabbitmq_hostname }}" - amqp_url: "pyamqp://galaxy_gpu:{{ rabbitmq_users_password.galaxy_gpu }}@{{ rabbitmq_hostname }}:5671/galaxy_gpu?ssl=1" + amqp_url: "pyamqp://pulsar:{{ rabbitmq_users_password.pulsar }}@{{ rabbitmq_hostname }}:5671/pulsar?ssl=1" amqp_acknowledge: true amqp_ack_republish_time: 1200 amqp_consumer_timeout: 2 amqp_publish_retry: true amqp_publish_retry_max_retries: 60 - manager: drmaa_gpu + manager: gpu # pulsar_runner: # load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner # galaxy_url: "https://{{ inventory_hostname }}" @@ -74,13 +75,13 @@ galaxy_job_config: runner: pulsar_runner default_file_action: remote_transfer dependency_resolution: remote - jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-test/files/staging" - persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-test/files/persistent" + jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/staging" + persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/persistent" remote_metadata: false rewrite_parameters: true transport: curl outputs_to_working_directory: false - submit_native_specification: '-l select=1:ncpus=2:mem=8gb:scratch_local=50gb -l walltime=12:00:00 -q galaxyeu@elixir-pbs.elixir-czech.cz' + # submit_native_specification: '-l select=1:ncpus=2:mem=8gb:scratch_local=50gb -l walltime=12:00:00 -q galaxyeu@elixir-pbs.elixir-czech.cz' singularity_enabled: true singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR" ## Following configuration works! @@ -98,6 +99,43 @@ galaxy_job_config: value: "$SCRATCHDIR" - name: TEMP value: "$SCRATCHDIR" + pulsar_gpu: + runner: pulsar_gpu_runner + default_file_action: remote_transfer + transport: curl + dependency_resolution: remote + jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/staging" + persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/persistent" + remote_metadata: false + rewrite_parameters: true + outputs_to_working_directory: false + singularity_enabled: true + singularity_run_extra_arguments: '--nv' + singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data:ro' + env: + # The cache directory holds the docker containers that get converted + - name: SINGULARITY_CACHEDIR + value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" + - name: APPTAINER_CACHEDIR + value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" + # Singularity uses a temporary directory to build the squashfs filesystem + - name: SINGULARITY_TMPDIR + value: "/storage/praha5-elixir/home/galaxyeu/singularity/tmp" + - name: APPTAINER_TMPDIR + value: "/storage/praha5-elixir/home/galaxyeu/singularity/tmp" + # Alphafold specific variables + - name: ALPHAFOLD_DB + value: "/storage/brno11-elixir/projects/alphafold/alphafold.db-2.3.1" + # Default variables + - name: TMPDIR + value: "$SCRATCHDIR" + - name: TMP + value: "$SCRATCHDIR" + - name: TEMP + value: "$SCRATCHDIR" + # Ensuring a consistent collation environment is good for reproducibility. + - name: LC_ALL + value: C tpv_dispatcher: runner: dynamic type: python @@ -121,6 +159,11 @@ galaxy_job_config: galaxy_config: galaxy: # Main Configuration + # To not bother the main disk + new_file_path: "/rbd/data/tmp" + nginx_upload_job_files_store: "/rbd/data/_upload_job_files" + nginx_upload_job_files_path: "/_job_files" + object_store_config_file: "{{ galaxy_config_dir }}/object_store_conf.xml" enable_oidc: true oidc_config_file: "{{ galaxy_config_dir }}/oidc_config.xml" oidc_backends_config_file: "{{ galaxy_config_dir }}/oidc_backends_config.xml" @@ -131,6 +174,8 @@ galaxy_config: - 499542@muni.cz - 325073@mail.muni.cz - demko@cesnet.cz + # cleanup_job: never + smtp_server: "rs.cesnet.cz:25" allow_user_creation: False database_connection: "postgresql:///{{ galaxy_db_name }}?host=/var/run/postgresql" file_path: /mnt/data/datasets @@ -139,6 +184,7 @@ galaxy_config: id_secret: "{{ vault_id_secret }}" job_config: "{{ galaxy_job_config }}" # Use the variable we defined above job_resource_params_file: "{{ galaxy_config_dir }}/job_resource_params_conf.xml" + sanitize_allowlist_file: "{{ galaxy_mutable_config_dir }}/sanitize_allowlist.txt" # SQL Performance slow_query_log_threshold: 5 enable_per_request_sql_debugging: true @@ -249,6 +295,8 @@ galaxy_config_templates: dest: "{{ galaxy_config_dir }}/oidc_config.xml" - src: templates/galaxy/config/oidc_backends_config.xml dest: "{{ galaxy_config_dir }}/oidc_backends_config.xml" + - src: templates/galaxy/config/object_store_conf.xml.j2 + dest: "{{ galaxy_config.galaxy.object_store_config_file }}" galaxy_extra_dirs: - /mnt/data @@ -360,11 +408,8 @@ rabbitmq_users: tags: administrator vhost: / - user: pulsar - password: "{{ rabbitmq_users_password.galaxy }}" + password: "{{ rabbitmq_users_password.pulsar }}" vhost: pulsar - - user: galaxy_gpu - password: "{{ rabbitmq_users_password.galaxy_gpu }}" - vhost: galaxy_gpu - user: galaxy password: "{{ vault_rabbitmq_password_galaxy }}" vhost: galaxy_internal @@ -375,7 +420,7 @@ rabbitmq_users: # TUS galaxy_tusd_port: 1080 -galaxy_tus_upload_store: /mnt/data/tus +galaxy_tus_upload_store: /rbd/data/tus # /mnt/data/tus #Redis galaxy_additional_venv_packages: diff --git a/group_vars/secret.yml b/group_vars/secret.yml index ac9fff7..dca1181 100644 --- a/group_vars/secret.yml +++ b/group_vars/secret.yml @@ -1,39 +1,44 @@ $ANSIBLE_VAULT;1.1;AES256 -34373839636536373136613934353239313537356130353038323138616661363538366635336362 -3030383330383837353763633034323532346536356630620a646636356565336530623663306232 -37386463633665656239353738613362613438663932396563616165323965303034633762636163 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+61623731623831616563366535636434303032353739306464653330396337633937636565633138 +34343630386466613763306234303361656366303335623334343962616235333561616138666635 +66336138303063383765383337383431633762363134316239383438373936333364636535383634 +36336333623235376434613839613831373165393333393737646230383134336131303463636330 +64326563343730666263366335626438356633656661636539323164366663323032313638366635 +653235323436333864303966653936343866 diff --git a/hosts b/hosts index 81236a7..20f29fa 100644 --- a/hosts +++ b/hosts @@ -1,9 +1,9 @@ [galaxyservers] -galaxy-cz.grid.cesnet.cz ansible_connection=local ansible_user=debian +usegalaxy.cz ansible_connection=local ansible_user=debian [dbservers:children] galaxyservers [monitoring] -galaxy-cz.grid.cesnet.cz ansible_connection=local ansible_user=debian +usegalaxy.cz ansible_connection=local ansible_user=debian [sentryservers] -galaxy-cz.grid.cesnet.cz ansible_connection=local ansible_user=debian +usegalaxy.cz ansible_connection=local ansible_user=debian diff --git a/roles/galaxyproject.nginx/tasks/apt.yml b/roles/galaxyproject.nginx/tasks/apt.yml index d86e036..b1e7118 100644 --- a/roles/galaxyproject.nginx/tasks/apt.yml +++ b/roles/galaxyproject.nginx/tasks/apt.yml @@ -1,10 +1,10 @@ --- -- name: Install nginx (APT) - apt: - pkg: nginx-{{ nginx_flavor }} - notify: - - restart nginx +# - name: Install nginx (APT) +# apt: +# pkg: nginx-{{ nginx_flavor }} +# notify: +# - restart nginx - name: Disable default vhost file: diff --git a/roles/galaxyproject.tusd/defaults/main.yml b/roles/galaxyproject.tusd/defaults/main.yml index 3633d0b..f9f4107 100644 --- a/roles/galaxyproject.tusd/defaults/main.yml +++ b/roles/galaxyproject.tusd/defaults/main.yml @@ -2,7 +2,7 @@ # Use 'latest' to install the latest (stable) release from https://github.com/tus/tusd/releases/, or a valid tag for a # specific tagged release (e.g. v1.7.3) -tusd_version: v1.6.0 +tusd_version: v1.8.0 # Path of the tusd binary tusd_path: /usr/local/sbin/tusd diff --git a/roles/usegalaxy_eu.certbot/tasks/renew-cron.yml b/roles/usegalaxy_eu.certbot/tasks/renew-cron.yml index c7197a5..8fe6aed 100644 --- a/roles/usegalaxy_eu.certbot/tasks/renew-cron.yml +++ b/roles/usegalaxy_eu.certbot/tasks/renew-cron.yml @@ -3,7 +3,7 @@ ansible.builtin.cron: name: Certbot automatic renewal. cron_file: "{{ certbot_auto_renew_cron_file | default(omit) }}" - job: "{{ certbot_script }} renew --quiet --no-self-upgrade {{ certbot_auto_renew_extra }}" + job: "{{ certbot_script }} renew --quiet {{ '--no-self-upgrade' if 'certbot-auto' in certbot_script else '' }} {{ certbot_auto_renew_extra }}" minute: "{{ certbot_auto_renew_minute }}" hour: "{{ certbot_auto_renew_hour }}" user: "{{ certbot_auto_renew_user }}" diff --git a/templates/galaxy/config/object_store_conf.xml.j2 b/templates/galaxy/config/object_store_conf.xml.j2 new file mode 100644 index 0000000..290d799 --- /dev/null +++ b/templates/galaxy/config/object_store_conf.xml.j2 @@ -0,0 +1,14 @@ + + + + + + + + + + + + + + diff --git a/templates/galaxy/config/oidc_backends_config.xml b/templates/galaxy/config/oidc_backends_config.xml index ac19887..75b935d 100644 --- a/templates/galaxy/config/oidc_backends_config.xml +++ b/templates/galaxy/config/oidc_backends_config.xml @@ -3,8 +3,15 @@ {{ e_infra_client_id }} {{ e_infra_client_secret }} - https://usegalaxy-test.cerit-sc.cz/authnz/keycloak/callback + https://{{ inventory_hostname }}/authnz/keycloak/callback https://login.e-infra.cz/oidc https://www.e-infra.cz/img/logo.svg + + {{ elixir_client_id }} + {{ elixir_client_secret }} + https://{{ inventory_hostname }}/authnz/elixir/callback + https://login.e-infra.cz/oidc + https://lifescience-ri.eu/fileadmin/lifescience-ri/media/Images/login-grey-wide.jpg.png + diff --git a/templates/nginx/galaxy.j2 b/templates/nginx/galaxy.j2 index a13184c..9009161 100644 --- a/templates/nginx/galaxy.j2 +++ b/templates/nginx/galaxy.j2 @@ -15,19 +15,41 @@ server { # Our log files will go to journalctl access_log syslog:server=unix:/dev/log; error_log syslog:server=unix:/dev/log; + # client_body_temp_path /rbd/data/nginx_upload_store; + client_body_buffer_size 1024m; + client_max_body_size 20G; # The most important location block, by default all requests are sent to gunicorn # If you serve galaxy at a path like /galaxy, change that below (and all other locations!) location / { # This is the backend to send the requests to. proxy_pass http://galaxy; - proxy_set_header Host $http_host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; proxy_set_header X-Forwarded-Proto $scheme; proxy_set_header Upgrade $http_upgrade; } + location /_job_files { + if ($request_method != POST) { + rewrite "" /api/jobs/$arg_job_id/files last; + } + upload_store {{ galaxy_config['galaxy']['nginx_upload_job_files_store'] }}; + # the rate limit might be needed if we have many Pulsar jobs that are writing data back + # we need to limit it because the disc IO can be too large, ideally this happens on a different node + # upload_limit_rate 32k; + upload_store_access user:rw group:rw all:rw; + upload_pass_form_field ""; + upload_set_form_field "__${upload_field_name}_path" "$upload_tmp_path"; + upload_pass_args on; + upload_pass /_upload_job_files_done; + } + + location /_upload_job_files_done { + internal; + rewrite "" /api/jobs/$arg_job_id/files; + } + location /api/upload/resumable_upload { # Disable request and response buffering proxy_request_buffering off; From 0cf7ec2a86805c205172a5567ca853be1ee57ace Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Boris=20Juri=C4=8D?= <74237898+BorisYourich@users.noreply.github.com> Date: Tue, 12 Sep 2023 15:47:27 +0200 Subject: [PATCH 4/8] Update README.md --- README.md | 30 ++++++++++++++++++++++++++++-- 1 file changed, 28 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index b019ec1..2a87bff 100644 --- a/README.md +++ b/README.md @@ -73,12 +73,14 @@ The api key can be found in the User -> Preferences -> Manage API Key in Galaxy Later we should use this [role](https://github.com/galaxyproject/ansible-galaxy-tools) to automate this, but there are too many tools to be installed and it is very inpractical for testing purposes. -## Notes +## Debian 11 + +### TUS On ubuntu < 22.04 and Debian < 12 the GLIBC version is incompatible with the ```galaxyproject.tusd``` GLIBC, therfore playbook ends in error. - in `roles/galaxyproject.tusd/defaults/main.yml` you have to set the `tusd_version:` to 'v1.8.0' (tested, possibly higher) -# Debian 11 +### Ansible On Debian 11 the default version of `ansible` is 2.10.08 which fails to extract binaries for TUSd. - workaround: @@ -87,8 +89,32 @@ On Debian 11 the default version of `ansible` is 2.10.08 which fails to extract - followed by `sudo apt-get update` and `sudo apt-get install ansible -y` - Note that you might need to `sudo apt remove ansible` `sudo apt autoremove` before you try to install ansible. +### Nginx Upload Module + +Our playbook makes use of `nginx-upload-module`, which is not included by default in any nginx-* distribution from `apt`. +This is a simple recipe for installing nginx with the upload-module. + +``` +sudo apt remove *nginx* -y && +sudo apt autoremove -y && + +wget http://nginx.org/download/nginx-1.24.0.tar.gz && +tar -xzf nginx-1.24.0.tar.gz && +cd nginx-1.24.0/ && +git clone https://github.com/hongzhidao/nginx-upload-module.git && +sudo apt-get install -y libpcre3 libpcre3-dev libssl-dev && +./configure --user=nginx --group=nginx --prefix=/etc/nginx --conf-path=/etc/nginx/nginx.conf --sbin-path=/usr/sbin/nginx --http-log-path=/var/log/nginx/access.log --error-log-path=/var/log/nginx/error.log --lock-path=/var/lock/nginx.lock --pid-path=/run/nginx.pid --modules-path=/usr/lib/nginx/modules --http-client-body-temp-path=/var/lib/nginx/body --http-fastcgi-temp-path=/var/lib/nginx/fastcgi --http-proxy-temp-path=/var/lib/nginx/proxy --http-scgi-temp-path=/var/lib/nginx/scgi --http-uwsgi-temp-path=/var/lib/nginx/uwsgi --with-compat --with-debug --with-pcre-jit --with-http_ssl_module --with-http_stub_status_module --with-http_realip_module --with-http_auth_request_module --with-http_v2_module --with-http_dav_module --with-http_slice_module --with-threads --with-http_addition_module --with-http_gunzip_module --with-http_gzip_static_module --with-http_sub_module --add-module=nginx-upload-module && +make && make install +``` + +Note that you might need to `sudo systemctl unmask nginx.service` and remove the `galaxy` and `redirect-ssl` from `/etc/nginx/sites-available and `/etc/nginx/sites-enabled` before running the playbook again. + +### Other issues + + Use `sudo apt install python3-docker` before running the `usegalaxy.rabbitmqserver` role. For influxdb apt key error: https://www.influxdata.com/blog/linux-package-signing-key-rotation/ For proftpd add "LoadModule mod_tls.c" to roles/galaxyproject.proftpd/templates/tls.conf.j2 just before the TLSEngine + From 2f8e01dfcbf71bbede8508fc0ebf974b942094e0 Mon Sep 17 00:00:00 2001 From: root Date: Wed, 13 Sep 2023 11:57:24 +0200 Subject: [PATCH 5/8] Add E-infra users to E-infra group rutine setup --- files/galaxy/welcome.html | 9 ++-- galaxy.yml | 10 +++- group_vars/galaxyservers.yml | 5 +- group_vars/secret.yml | 88 ++++++++++++++++++------------------ 4 files changed, 61 insertions(+), 51 deletions(-) diff --git a/files/galaxy/welcome.html b/files/galaxy/welcome.html index 3be12bc..549c600 100644 --- a/files/galaxy/welcome.html +++ b/files/galaxy/welcome.html @@ -21,10 +21,11 @@

Welcome to UseGalaxy CZ



-

This service is part of the e-infra.cz infrastructure and Elixir Czech Republic.

-

-

Dear users, we are still in testing mode, so we kindly ask you to report any troubles at regalaxy@rt.cesnet.cz. So far, we know that a few tools are incompatible with the latest Galaxy version. Sometimes your jobs may end up in the Error state or even in the Complete state (but empty with 0 size) with messages like: =>> PBS: job killed:... That means the resources need to be fit to means of the tool, and reporting this fact will help us improve the service. On behalf of the admin group, thank you. -

+
+

This service is part of the e-infra.cz infrastructure and Elixir Czech Republic.

+
+
+

Please visit UseGalaxy CZ Documentation before using the service. If this is your first time using Galaxy platform, we strongly recommend taking an interactive tour which is enabled at the bottom of the page. In case of any further questions, please contact us at regalaxy@rt.cesnet.cz.



diff --git a/galaxy.yml b/galaxy.yml index 1a91bfe..5b9816d 100644 --- a/galaxy.yml +++ b/galaxy.yml @@ -29,7 +29,7 @@ mode: 0640 - name: Install Dependencies package: - name: ['acl', 'bzip2', 'git', 'make', 'tar', 'python3-venv', 'python3-setuptools'] + name: ['acl', 'bzip2', 'git', 'make', 'tar', 'python3-bioblend', 'python3-venv', 'python3-setuptools'] - name: Install RHEL/CentOS/Rocky specific dependencies package: name: ['tmpwatch'] @@ -88,4 +88,10 @@ minute: "0" hour: "0" job: "GALAXY_LOG_DIR=/tmp/gxadmin/ GALAXY_ROOT={{ galaxy_root }}/server /usr/local/bin/gxadmin galaxy cleanup 60" - + - name: Setup user - group association rutine + ansible.builtin.cron: + name: "Add E-infra users to E-infra group" + user: postgres # Run as the postgres user + minute: "0" + hour: "*" + job: "python3 {{ playbook_dir }}/add_group_users.py {{ inventory_hostname }} {{ api_key }}" diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index 3869017..b657dbb 100644 --- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -7,8 +7,8 @@ galaxy_manage_cleanup: true galaxy_layout: root-dir galaxy_root: /srv/galaxy galaxy_user: {name: "{{ galaxy_user_name }}", shell: /bin/bash} -galaxy_commit_id: 1ad49865fbeb03551cf7774dc0c12e5cd27ff797 # release_23.0 -#galaxy_commit_id: 72070dbd0a6d0f418d0b8f914825ea2b8e6a0a88 + # galaxy_commit_id: 1ad49865fbeb03551cf7774dc0c12e5cd27ff797 # release_23.0 +galaxy_commit_id: 72070dbd0a6d0f418d0b8f914825ea2b8e6a0a88 galaxy_force_checkout: true miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda" miniconda_version: 23.5.2 # 23.5.0 # 4.12.0 @@ -176,6 +176,7 @@ galaxy_config: - demko@cesnet.cz # cleanup_job: never smtp_server: "rs.cesnet.cz:25" + error_email_to: "regalaxy@rt.cesnet.cz" allow_user_creation: False database_connection: "postgresql:///{{ galaxy_db_name }}?host=/var/run/postgresql" file_path: /mnt/data/datasets diff --git a/group_vars/secret.yml b/group_vars/secret.yml index dca1181..eb3d58a 100644 --- a/group_vars/secret.yml +++ b/group_vars/secret.yml @@ -1,44 +1,46 @@ $ANSIBLE_VAULT;1.1;AES256 -35613465376632333130666438356137353563333166313263613533313234373234633232383637 -3935643031393433626439346338306166666234643533340a393834343765363532353961663663 -64613266393137643063646235666331303030636430356439663266343639666365383139353530 -6538613661643965380a666434646135383032393937363439656234653263633431366634616438 -36653064396661633934616634383866373564383233316430643339626466366464346465643839 -66393536646463353838323730633861633539656137666661303137306236366664393234353237 -39346164666234363736346639323266373736643333383362396562623662313532653031313466 -30303562363861613661326531663563313365323137366463626435646538313438646562303238 -66663636633037373365646432346565363839353938313439656333363963653164373330646238 -38626137333862376663313466386435316135626461376530643034653032353138343135363964 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+64653561363536366630653831633431613863646361353365316235393963663533636534326466 +31616230393936646635303235656563626531393235636262363063616461653963303632646136 +33326461323861646137616537623162653034656537333261366466356439313963623637346465 +31323938363164656261316538613538643733303439653662646637343964386561396337343533 +39363737653738663435646134653936363737306431323733376163633162393065313137666533 +32653763666264653263376563623866373635656436373364353336323531326432 From 3d4edad989c5d00ed3180f84675f074f7a0807e0 Mon Sep 17 00:00:00 2001 From: root Date: Wed, 13 Sep 2023 16:02:29 +0200 Subject: [PATCH 6/8] Fixed error with group users addition --- add_group_users.py | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100755 add_group_users.py diff --git a/add_group_users.py b/add_group_users.py new file mode 100755 index 0000000..51b46b2 --- /dev/null +++ b/add_group_users.py @@ -0,0 +1,36 @@ +import psycopg2 +import bioblend.galaxy +import sys + +conn = psycopg2.connect(database="galaxy", user="postgres") +cursor = conn.cursor() +cursor.execute("SELECT * FROM galaxy_user") +users = cursor.fetchall() +user_dict = dict() + +for user in users: + user_dict[user[0]] = user[3] # id is key, email is value + +cursor.execute("SELECT * FROM custos_authnz_token") +einfra_users = cursor.fetchall() + +einfra_emails = [] +for einfra_user in einfra_users: + einfra_emails.append(user_dict[einfra_user[1]]) + +server = 'https://' + sys.argv[1] +api_key = sys.argv[2] +gi = bioblend.galaxy.GalaxyInstance(url=server, key=api_key) + +api_users = gi.users.get_users() +id_dict = dict() +for user in api_users: + id_dict[user['email']] = user['id'] + +groups = gi.groups.get_groups() +for group in groups: + if group['name'] == 'E-infra': + group_id = group['id'] + +for mail in einfra_emails: + gi.groups.add_group_user(group_id=group_id, user_id=id_dict[mail]) From 2312bb771354d5fb19fe6497db2d1758e5d21718 Mon Sep 17 00:00:00 2001 From: martindemko <325073@mail.muni.cz> Date: Mon, 30 Oct 2023 11:17:10 +0100 Subject: [PATCH 7/8] Update README.md adds zlib1g-dev into README --- README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 2a87bff..1f2da4e 100644 --- a/README.md +++ b/README.md @@ -83,8 +83,9 @@ On ubuntu < 22.04 and Debian < 12 the GLIBC version is incompatible with the ``` ### Ansible On Debian 11 the default version of `ansible` is 2.10.08 which fails to extract binaries for TUSd. -- workaround: - - `sudo vim /etc/apt/sources.list` add this line : `deb http://ppa.launchpad.net/ansible/ansible/ubuntu focal main` +- workaround: + - because of Puppet, we need to create dedicated sources.list file for ansible + - `sudo vim /etc/apt/sources.list.d/ansible_ubuntu_focal_main.list` add this line : `deb http://ppa.launchpad.net/ansible/ansible/ubuntu focal main` - then `sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 93C4A3FD7BB9C367` - followed by `sudo apt-get update` and `sudo apt-get install ansible -y` - Note that you might need to `sudo apt remove ansible` `sudo apt autoremove` before you try to install ansible. @@ -102,7 +103,7 @@ wget http://nginx.org/download/nginx-1.24.0.tar.gz && tar -xzf nginx-1.24.0.tar.gz && cd nginx-1.24.0/ && git clone https://github.com/hongzhidao/nginx-upload-module.git && -sudo apt-get install -y libpcre3 libpcre3-dev libssl-dev && +sudo apt-get install -y libpcre3 libpcre3-dev libssl-dev zlib1g-dev && ./configure --user=nginx --group=nginx --prefix=/etc/nginx --conf-path=/etc/nginx/nginx.conf --sbin-path=/usr/sbin/nginx --http-log-path=/var/log/nginx/access.log --error-log-path=/var/log/nginx/error.log --lock-path=/var/lock/nginx.lock --pid-path=/run/nginx.pid --modules-path=/usr/lib/nginx/modules --http-client-body-temp-path=/var/lib/nginx/body --http-fastcgi-temp-path=/var/lib/nginx/fastcgi --http-proxy-temp-path=/var/lib/nginx/proxy --http-scgi-temp-path=/var/lib/nginx/scgi --http-uwsgi-temp-path=/var/lib/nginx/uwsgi --with-compat --with-debug --with-pcre-jit --with-http_ssl_module --with-http_stub_status_module --with-http_realip_module --with-http_auth_request_module --with-http_v2_module --with-http_dav_module --with-http_slice_module --with-threads --with-http_addition_module --with-http_gunzip_module --with-http_gzip_static_module --with-http_sub_module --add-module=nginx-upload-module && make && make install ``` From ced7ee795968c5c4cf7a2408842c0ed4de26d458 Mon Sep 17 00:00:00 2001 From: martindemko <325073@mail.muni.cz> Date: Mon, 15 Jan 2024 10:52:39 +0100 Subject: [PATCH 8/8] starting modifications for galaxy-umsa --- ansible.cfg | 8 +- galaxy.yml | 94 +++++- group_vars/all.yml | 5 +- group_vars/dbservers.yml | 46 +-- group_vars/galaxyservers.yml | 299 +++++++++--------- group_vars/secret.yml | 74 ++--- hosts | 8 +- .../galaxyproject.nginx/tasks/ssl-common.yml | 11 + .../defaults/main.yml | 2 +- .../galaxy/config/object_store_conf.xml.j2 | 9 +- .../galaxy/config/oidc_backends_config.xml | 7 - .../galaxy/config/sanitize_allowlist.txt | 1 + templates/nginx/galaxy.j2 | 92 ++---- 13 files changed, 324 insertions(+), 332 deletions(-) create mode 100644 templates/galaxy/config/sanitize_allowlist.txt diff --git a/ansible.cfg b/ansible.cfg index bc40777..1a43c9d 100644 --- a/ansible.cfg +++ b/ansible.cfg @@ -1,14 +1,16 @@ [defaults] interpreter_python = /usr/bin/python3 inventory = hosts +bin_ansible_callbacks = True retry_files_enabled = false vault_password_file = .vault-password.txt gather_subset=!hardware -no_log = True +#no_log = True +log_path = /var/log/ansible.log # Show diffs of changes [diff] -always = False +always = True [ssh_connection] -pipelining = true +pipelining = True diff --git a/galaxy.yml b/galaxy.yml index 5b9816d..304e356 100644 --- a/galaxy.yml +++ b/galaxy.yml @@ -5,12 +5,46 @@ pre_tasks: - name: Install Dependencies package: - name: 'acl' + name: ['acl', 'logrotate'] roles: - galaxyproject.postgresql - role: galaxyproject.postgresql_objects become: true become_user: postgres + post_tasks: + - name: Create pg_dump backup folder if needed + file: + path: "{{ postgresql_backup_dir }}/pg_dump" + state: directory + owner: postgres + group: "{{ galaxy_user_group }}" + mode: 0750 + - name: Create initial empty pg_dump file if needed # otherwise the following logrotate conf will not work + file: + path: "{{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql.gz" + state: touch + owner: postgres + group: "{{ galaxy_user_group }}" + mode: 0640 + - name: Set-up Galaxy DB backup using pg_dump and logrotate + ansible.builtin.blockinfile: + path: "/etc/logrotate.d/{{ postgresql_pg_dump_prefix }}" + create: true + block: | + {{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql.gz { + daily + missingok + rotate 14 + nocompress + nocreate + postrotate + echo "### Start backup at `date` ###" >> /var/log/{{ postgresql_pg_dump_prefix }}_errors.log + sudo -u postgres pg_dump {{ galaxy_db_name }} --file={{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql --verbose >> /var/log/{{ postgresql_pg_dump_prefix }}_errors.log 2>&1 + sudo chmod 640 {{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql >> /var/log/{{ postgresql_pg_dump_prefix }}_errors.log 2>&1 + sudo -u postgres gzip {{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql >> /var/log/{{ postgresql_pg_dump_prefix }}_errors.log 2>&1 + echo "### Finished backup at `date` ###" >> /var/log/{{ postgresql_pg_dump_prefix }}_errors.log + endscript + } - hosts: galaxyservers become: true @@ -18,7 +52,11 @@ vars_files: - group_vars/secret.yml pre_tasks: - - pip: + - name: Install Dependencies + ansible.builtin.package: + name: ['acl', 'bzip2', 'git', 'make', 'tar', 'python3-bioblend', 'python3-venv', 'python3-setuptools', 'python3-pip', 'python3-psycopg2', 'rsync', 'python3-docker', 'nginx-full'] + - name: Install additional pip packages + ansible.builtin.pip: name: passlib - htpasswd: path: /etc/nginx/passwd @@ -27,9 +65,6 @@ owner: www-data # nginx on centos group: root mode: 0640 - - name: Install Dependencies - package: - name: ['acl', 'bzip2', 'git', 'make', 'tar', 'python3-bioblend', 'python3-venv', 'python3-setuptools'] - name: Install RHEL/CentOS/Rocky specific dependencies package: name: ['tmpwatch'] @@ -38,30 +73,57 @@ package: name: ['tmpreaper'] when: ansible_os_family == 'Debian' + - name: Ensure the python command exists + ansible.builtin.shell: + cmd: which python||exit 0 + register: python_path + - name: Register python3 path + ansible.builtin.command: which python3 + register: python3_path + when: python_path.stdout == "" + - name: Link python to python3 if missing + ansible.builtin.file: + src: python3_path.stdout + dest: python3_path.stdout[:-1] + state: link + force: yes + when: python_path.stdout == "" - git: repo: 'https://github.com/usegalaxy-eu/libraries-training-repo' dest: /libraries/ + when: "'usegalaxy' in inventory_hostname" +# - name: Create data storage for UMSA +# file: +# owner: "{{ galaxy_user_name }}" +# group: "{{ galaxy_user_group }}" +# path: "{{ galaxy_data_prefix }}" +# state: directory +# mode: "0755" +# when: "'umsa' in inventory_hostname" - name: Create the RBD storage directory file: - owner: galaxy - group: galaxy + owner: "{{ galaxy_user_name }}" + group: "{{ galaxy_user_group }}" path: /rbd/data state: directory mode: '0755' + when: "'usegalaxy' in inventory_hostname" - name: Create the nginx upload job files store file: owner: www-data - group: galaxy + group: "{{ galaxy_user_group }}" path: /rbd/data/_upload_job_files state: directory mode: '0775' + when: "'usegalaxy' in inventory_hostname" - name: Create the client body temp path file: owner: www-data - group: galaxy + group: "{{ galaxy_user_group }}" path: /rbd/data/nginx_upload_store state: directory mode: '0775' + when: "'usegalaxy' in inventory_hostname" roles: - galaxyproject.tusd - usegalaxy_eu.apptainer @@ -76,15 +138,15 @@ - galaxyproject.proftpd - geerlingguy.docker - usegalaxy_eu.rabbitmqserver - - galaxyproject.tiaas2 +# - galaxyproject.tiaas2 - galaxyproject.gxadmin - galaxyproject.cvmfs - - dj-wasabi.telegraf +# - dj-wasabi.telegraf post_tasks: - name: Setup gxadmin cleanup task ansible.builtin.cron: name: "Cleanup Old User Data" - user: galaxy # Run as the Galaxy user + user: "{{ galaxy_user_name }}" # Run as the Galaxy user minute: "0" hour: "0" job: "GALAXY_LOG_DIR=/tmp/gxadmin/ GALAXY_ROOT={{ galaxy_root }}/server /usr/local/bin/gxadmin galaxy cleanup 60" @@ -95,3 +157,11 @@ minute: "0" hour: "*" job: "python3 {{ playbook_dir }}/add_group_users.py {{ inventory_hostname }} {{ api_key }}" + when: "'usegalaxy' in inventory_hostname" + - name: RE Galaxy instance patch in lib/galaxy/webapps/galaxy/api/job_files.py + replace: + path: "{{ galaxy_root }}/server/lib/galaxy/webapps/galaxy/api/job_files.py" + regexp: '^(\s*?)shutil\.move\(input_file\.name,\s*path\)\s*$' + replace: '\1os.chmod(shutil.move(input_file.name, path), 0o664)' + validate: 'python -m py_compile %s' + when: "'galaxy-re' in inventory_hostname or 'galaxy-re' in ansible_hostname" diff --git a/group_vars/all.yml b/group_vars/all.yml index a36f40d..6b084d5 100644 --- a/group_vars/all.yml +++ b/group_vars/all.yml @@ -3,8 +3,11 @@ pip_virtualenv_command: /usr/bin/python3 -m venv # usegalaxy_eu.certbot, usegalaxy_eu.tiaas2, galaxyproject.galaxy # Common variables needed by all hosts -galaxy_user_name: galaxy +galaxy_user_name: galaxyumsa +galaxy_user_id: 10456 +galaxy_user_group: galaxyumsa galaxy_db_name: galaxy +galaxy_data_prefix: "/mnt/data" # CVMFS vars cvmfs_role: client diff --git a/group_vars/dbservers.yml b/group_vars/dbservers.yml index 2504faf..0082b0f 100644 --- a/group_vars/dbservers.yml +++ b/group_vars/dbservers.yml @@ -13,28 +13,28 @@ postgresql_objects_privileges: privs: SELECT objs: ALL_IN_SCHEMA - - database: galaxy - roles: tiaas - objs: galaxy_user,galaxy_session,job,history,workflow,workflow_invocation - type: table - privs: SELECT - - database: galaxy - roles: tiaas - objs: user_group_association,galaxy_group,role,group_role_association - type: table - privs: SELECT,INSERT - - database: galaxy - roles: tiaas - objs: group_role_association - type: table - privs: DELETE - - database: galaxy - roles: tiaas - objs: role_id_seq,galaxy_group_id_seq,group_role_association_id_seq,user_group_association_id_seq - type: sequence - privs: USAGE,SELECT +# - database: galaxy +# roles: tiaas +# objs: galaxy_user,galaxy_session,job,history,workflow,workflow_invocation +# type: table +# privs: SELECT +# - database: galaxy +# roles: tiaas +# objs: user_group_association,galaxy_group,role,group_role_association +# type: table +# privs: SELECT,INSERT +# - database: galaxy +# roles: tiaas +# objs: group_role_association +# type: table +# privs: DELETE +# - database: galaxy +# roles: tiaas +# objs: role_id_seq,galaxy_group_id_seq,group_role_association_id_seq,user_group_association_id_seq +# type: sequence +# privs: USAGE,SELECT # PostgreSQL Backups -postgresql_backup_dir: /data/backups -postgresql_backup_local_dir: "{{ '~postgres' | expanduser }}/backups" - +postgresql_backup_dir: "{{ galaxy_data_prefix }}/backups" +postgresql_backup_local_dir: "{{ galaxy_data_prefix }}/backups/scripts" +postgresql_pg_dump_prefix: galaxy_db_backup diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index b657dbb..35d031d 100644 --- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -6,13 +6,19 @@ galaxy_manage_paths: true # False by default as your administrator might e.g. ha galaxy_manage_cleanup: true galaxy_layout: root-dir galaxy_root: /srv/galaxy -galaxy_user: {name: "{{ galaxy_user_name }}", shell: /bin/bash} - # galaxy_commit_id: 1ad49865fbeb03551cf7774dc0c12e5cd27ff797 # release_23.0 +galaxy_tool_dependency_dir: "{{ galaxy_mutable_data_dir }}/dependencies" +galaxy_user: + name: "{{ galaxy_user_name }}" + uid: "{{ galaxy_user_id }}" + group: "{{ galaxy_user_group }}" + shell: /bin/bash +# galaxy_commit_id: 1ad49865fbeb03551cf7774dc0c12e5cd27ff797 # release_23.0 galaxy_commit_id: 72070dbd0a6d0f418d0b8f914825ea2b8e6a0a88 galaxy_force_checkout: true miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda" -miniconda_version: 23.5.2 # 23.5.0 # 4.12.0 -miniconda_channels: ['conda-forge', 'defaults'] +miniconda_version: 'latest' # 23.5.2 # 23.5.0 # 4.12.0 +miniconda_channels: ['conda-forge', 'bioconda', 'anaconda', 'defaults'] +miniconda_base_env_packages: ['mamba'] # Galaxy Job Configuration galaxy_job_config: @@ -20,30 +26,30 @@ galaxy_job_config: local_runner: load: galaxy.jobs.runners.local:LocalJobRunner workers: 4 - pulsar_runner: - load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner - galaxy_url: "https://{{ rabbitmq_hostname }}" - amqp_url: "pyamqp://pulsar:{{ rabbitmq_users_password.pulsar }}@{{ rabbitmq_hostname }}:5671/pulsar?ssl=1" - amqp_acknowledge: true - amqp_ack_republish_time: 1200 - amqp_consumer_timeout: 2 - amqp_publish_retry: true - amqp_publish_retry_max_retries: 60 - manager: _default_ - pulsar_gpu_runner: - load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner - galaxy_url: "https://{{ rabbitmq_hostname }}" - amqp_url: "pyamqp://pulsar:{{ rabbitmq_users_password.pulsar }}@{{ rabbitmq_hostname }}:5671/pulsar?ssl=1" - amqp_acknowledge: true - amqp_ack_republish_time: 1200 - amqp_consumer_timeout: 2 - amqp_publish_retry: true - amqp_publish_retry_max_retries: 60 - manager: gpu + #pulsar_runner: + # load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner + # galaxy_url: "https://{{ rabbitmq_hostname }}" + # amqp_url: "pyamqp://pulsar:{{ vault_rabbitmq_password.pulsar }}@{{ rabbitmq_hostname }}:5671/pulsar?ssl=1" + # amqp_acknowledge: true + # amqp_ack_republish_time: 1200 + # amqp_consumer_timeout: 2 + # amqp_publish_retry: true + # amqp_publish_retry_max_retries: 60 + # manager: _default_ + #pulsar_gpu_runner: + # load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner + # galaxy_url: "https://{{ rabbitmq_hostname }}" + # amqp_url: "pyamqp://pulsar:{{ vault_rabbitmq_password.pulsar }}@{{ rabbitmq_hostname }}:5671/pulsar?ssl=1" + # amqp_acknowledge: true + # amqp_ack_republish_time: 1200 + # amqp_consumer_timeout: 2 + # amqp_publish_retry: true + # amqp_publish_retry_max_retries: 60 + # manager: gpu # pulsar_runner: # load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner # galaxy_url: "https://{{ inventory_hostname }}" - # amqp_url: "pyamqp://pulsar:{{ rabbitmq_users_password.galaxy }}@{{ inventory_hostname }}:5671/pulsar?ssl=1" + # amqp_url: "pyamqp://pulsar:{{ vault_rabbitmq_password.galaxy }}@{{ inventory_hostname }}:5671/pulsar?ssl=1" # amqp_acknowledge: true # amqp_ack_republish_time: 1200 # amqp_consumer_timeout: 2 @@ -53,7 +59,8 @@ galaxy_job_config: handling: assign: ['db-skip-locked'] execution: - default: tpv_dispatcher + default: local_env + #default: tpv_dispatcher environments: local_env: runner: local_runner @@ -71,71 +78,71 @@ galaxy_job_config: # Apptainer uses a temporary directory to build the squashfs filesystem - name: APPTAINER_TMPDIR value: /tmp - pulsar: - runner: pulsar_runner - default_file_action: remote_transfer - dependency_resolution: remote - jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/staging" - persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/persistent" - remote_metadata: false - rewrite_parameters: true - transport: curl - outputs_to_working_directory: false - # submit_native_specification: '-l select=1:ncpus=2:mem=8gb:scratch_local=50gb -l walltime=12:00:00 -q galaxyeu@elixir-pbs.elixir-czech.cz' - singularity_enabled: true - singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR" - ## Following configuration works! - # singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro" - container_resolvers: - - type: explicit_singularity - - type: mulled_singularity - env: - # Ensuring a consistent collation environment is good for reproducibility. - - name: LC_ALL - value: C - - name: TMPDIR - value: "$SCRATCHDIR" - - name: TMP - value: "$SCRATCHDIR" - - name: TEMP - value: "$SCRATCHDIR" - pulsar_gpu: - runner: pulsar_gpu_runner - default_file_action: remote_transfer - transport: curl - dependency_resolution: remote - jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/staging" - persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/persistent" - remote_metadata: false - rewrite_parameters: true - outputs_to_working_directory: false - singularity_enabled: true - singularity_run_extra_arguments: '--nv' - singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data:ro' - env: - # The cache directory holds the docker containers that get converted - - name: SINGULARITY_CACHEDIR - value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" - - name: APPTAINER_CACHEDIR - value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" - # Singularity uses a temporary directory to build the squashfs filesystem - - name: SINGULARITY_TMPDIR - value: "/storage/praha5-elixir/home/galaxyeu/singularity/tmp" - - name: APPTAINER_TMPDIR - value: "/storage/praha5-elixir/home/galaxyeu/singularity/tmp" - # Alphafold specific variables - - name: ALPHAFOLD_DB - value: "/storage/brno11-elixir/projects/alphafold/alphafold.db-2.3.1" - # Default variables - - name: TMPDIR - value: "$SCRATCHDIR" - - name: TMP - value: "$SCRATCHDIR" - - name: TEMP - value: "$SCRATCHDIR" - # Ensuring a consistent collation environment is good for reproducibility. - - name: LC_ALL - value: C +# pulsar: +# runner: pulsar_runner +# default_file_action: remote_transfer +# dependency_resolution: remote +# jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/staging" +# persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/persistent" +# remote_metadata: false +# rewrite_parameters: true +# transport: curl +# outputs_to_working_directory: false +# # submit_native_specification: '-l select=1:ncpus=2:mem=8gb:scratch_local=50gb -l walltime=12:00:00 -q galaxyeu@elixir-pbs.elixir-czech.cz' +# singularity_enabled: true +# singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR" +# ## Following configuration works! +# # singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro" +# container_resolvers: +# - type: explicit_singularity +# - type: mulled_singularity +# env: +# # Ensuring a consistent collation environment is good for reproducibility. +# - name: LC_ALL +# value: C +# - name: TMPDIR +# value: "$SCRATCHDIR" +# - name: TMP +# value: "$SCRATCHDIR" +# - name: TEMP +# value: "$SCRATCHDIR" +# pulsar_gpu: +# runner: pulsar_gpu_runner +# default_file_action: remote_transfer +# transport: curl +# dependency_resolution: remote +# jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/staging" +# persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/persistent" +# remote_metadata: false +# rewrite_parameters: true +# outputs_to_working_directory: false +# singularity_enabled: true +# singularity_run_extra_arguments: '--nv' +# singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data:ro' +# env: +# # The cache directory holds the docker containers that get converted +# - name: SINGULARITY_CACHEDIR +# value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" +# - name: APPTAINER_CACHEDIR +# value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" +# # Singularity uses a temporary directory to build the squashfs filesystem +# - name: SINGULARITY_TMPDIR +# value: "/storage/praha5-elixir/home/galaxyeu/singularity/tmp" +# - name: APPTAINER_TMPDIR +# value: "/storage/praha5-elixir/home/galaxyeu/singularity/tmp" +# # Alphafold specific variables +# - name: ALPHAFOLD_DB +# value: "/storage/brno11-elixir/projects/alphafold/alphafold.db-2.3.1" +# # Default variables +# - name: TMPDIR +# value: "$SCRATCHDIR" +# - name: TMP +# value: "$SCRATCHDIR" +# - name: TEMP +# value: "$SCRATCHDIR" +# # Ensuring a consistent collation environment is good for reproducibility. +# - name: LC_ALL +# value: C tpv_dispatcher: runner: dynamic type: python @@ -144,24 +151,18 @@ galaxy_job_config: tpv_config_files: - https://raw.githubusercontent.com/galaxyproject/tpv-shared-database/main/tools.yml - "{{ tpv_config_dir }}/tpv_rules_local.yml" - resources: - default: default - groups: - default: [] - testing: [cores, time] tools: - class: local # these special tools that aren't parameterized for remote execution - expression tools, upload, etc environment: local_env - id: testing environment: tpv_dispatcher - resources: testing galaxy_config: galaxy: # Main Configuration # To not bother the main disk - new_file_path: "/rbd/data/tmp" - nginx_upload_job_files_store: "/rbd/data/_upload_job_files" + new_file_path: "{{ galaxy_data_prefix }}/tmp" + nginx_upload_job_files_store: "{{ galaxy_data_prefix }}/_upload_job_files" nginx_upload_job_files_path: "/_job_files" object_store_config_file: "{{ galaxy_config_dir }}/object_store_conf.xml" enable_oidc: true @@ -174,13 +175,12 @@ galaxy_config: - 499542@muni.cz - 325073@mail.muni.cz - demko@cesnet.cz - # cleanup_job: never smtp_server: "rs.cesnet.cz:25" error_email_to: "regalaxy@rt.cesnet.cz" allow_user_creation: False database_connection: "postgresql:///{{ galaxy_db_name }}?host=/var/run/postgresql" - file_path: /mnt/data/datasets - job_working_directory: /mnt/data/jobs + file_path: "{{ galaxy_data_prefix }}/datasets" + job_working_directory: "{{ galaxy_data_prefix }}/jobs" object_store_store_by: uuid id_secret: "{{ vault_id_secret }}" job_config: "{{ galaxy_job_config }}" # Use the variable we defined above @@ -217,18 +217,18 @@ galaxy_config: dependency_resolvers_config_file: "{{ galaxy_config_dir }}/dependency_resolvers_conf.xml" containers_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml" # Data Library Directories - library_import_dir: /libraries/admin - user_library_import_dir: /libraries/user +# library_import_dir: /libraries/admin +# user_library_import_dir: /libraries/user # Celery - amqp_internal_connection: "pyamqp://galaxy:{{ vault_rabbitmq_password_galaxy }}@localhost:5671/galaxy_internal?ssl=1" + amqp_internal_connection: "pyamqp://galaxy:{{ vault_rabbitmq_password.galaxy }}@localhost:5671/galaxy_internal?ssl=1" celery_conf: result_backend: "redis://localhost:6379/0" enable_celery_tasks: true # Monitoring - statsd_host: localhost - statsd_influxdb: true +# statsd_host: localhost +# statsd_influxdb: true # FTP - ftp_upload_dir: /mnt/data/uploads + ftp_upload_dir: "{{ galaxy_data_prefix}}/uploads" ftp_upload_site: "{{ inventory_hostname }}" gravity: process_manager: systemd @@ -265,21 +265,21 @@ galaxy_config: pools: - job-handlers - workflow-schedulers - reports: - enable: true - url_prefix: /reports - bind: "unix:{{ galaxy_mutable_config_dir }}/reports.sock" - config_file: "{{ galaxy_config_dir }}/reports.yml" +# reports: +# enable: false +# url_prefix: /reports +# bind: "unix:{{ galaxy_mutable_config_dir }}/reports.sock" +# config_file: "{{ galaxy_config_dir }}/reports.yml" galaxy_job_config_file: "{{ galaxy_config_dir }}/galaxy.yml" -galaxy_config_files_public: - - src: files/galaxy/welcome.html - dest: "{{ galaxy_mutable_config_dir }}/welcome.html" +#galaxy_config_files_public: +# - src: files/galaxy/welcome.html +# dest: "{{ galaxy_mutable_config_dir }}/welcome.html" galaxy_config_files: - - src: files/galaxy/themes.yml - dest: "{{ galaxy_config.galaxy.themes_config_file }}" +# - src: files/galaxy/themes.yml +# dest: "{{ galaxy_config.galaxy.themes_config_file }}" - src: files/galaxy/config/tpv_rules_local.yml dest: "{{ tpv_mutable_dir }}/tpv_rules_local.yml" @@ -290,8 +290,10 @@ galaxy_config_templates: dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}" - src: templates/galaxy/config/job_resource_params_conf.xml.j2 dest: "{{ galaxy_config.galaxy.job_resource_params_file }}" - - src: templates/galaxy/config/reports.yml - dest: "{{ galaxy_config.gravity.reports.config_file }}" + - src: templates/galaxy/config/sanitize_allowlist.txt + dest: "{{ galaxy_config.galaxy.sanitize_allowlist_file }}" +# - src: templates/galaxy/config/reports.yml +# dest: "{{ galaxy_config.gravity.reports.config_file }}" - src: templates/galaxy/config/oidc_config.xml dest: "{{ galaxy_config_dir }}/oidc_config.xml" - src: templates/galaxy/config/oidc_backends_config.xml @@ -300,7 +302,7 @@ galaxy_config_templates: dest: "{{ galaxy_config.galaxy.object_store_config_file }}" galaxy_extra_dirs: - - /mnt/data + - "{{ galaxy_data_prefix }}" - "{{ galaxy_config_dir }}/{{ tpv_config_dir_name }}" galaxy_extra_privsep_dirs: @@ -338,7 +340,7 @@ nginx_servers: - redirect-ssl nginx_ssl_servers: - galaxy - # - sentry +# - sentry nginx_enable_default_server: false nginx_conf_http: client_max_body_size: 1g @@ -400,28 +402,27 @@ rabbitmq_config: rabbitmq_vhosts: - pulsar - - galaxy_gpu - galaxy_internal rabbitmq_users: - user: debian - password: "{{ rabbitmq_users_password.mqadmin }}" + password: "{{ vault_rabbitmq_password.mqadmin }}" tags: administrator vhost: / - user: pulsar - password: "{{ rabbitmq_users_password.pulsar }}" + password: "{{ vault_rabbitmq_password.pulsar }}" vhost: pulsar - user: galaxy - password: "{{ vault_rabbitmq_password_galaxy }}" + password: "{{ vault_rabbitmq_password.galaxy }}" vhost: galaxy_internal - user: flower - password: "{{ vault_rabbitmq_password_flower }}" + password: "{{ vault_rabbitmq_password.flower }}" tags: administrator vhost: galaxy_internal # TUS galaxy_tusd_port: 1080 -galaxy_tus_upload_store: /rbd/data/tus # /mnt/data/tus +galaxy_tus_upload_store: "{{ galaxy_data_prefix }}/tus" # /mnt/data/tus #Redis galaxy_additional_venv_packages: @@ -429,44 +430,27 @@ galaxy_additional_venv_packages: # Flower flower_python_version: python3 +flower_bind_interface: localhost +flower_port: 5555 flower_app_dir: "{{ galaxy_root }}" flower_python_path: "{{ galaxy_root }}/server/lib" flower_venv_dir: "{{ galaxy_venv_dir }}" flower_app_name: galaxy.celery flower_db_file: "{{ galaxy_root }}/var/flower.db" flower_persistent: true -flower_broker_api: "https://flower:{{ vault_rabbitmq_password_flower }}@localhost:5671/api/" -flower_broker_url: "amqp://flower:{{ vault_rabbitmq_password_flower }}@localhost:5671/galaxy_internal?ssl=true" +flower_broker_api: "https://flower:{{ vault_rabbitmq_password.flower }}@localhost:5671/api/" +flower_broker_url: "pyamqp://flower:{{ vault_rabbitmq_password.flower }}@localhost:5671/galaxy_internal?ssl=1" +#flower_broker_url: "pyamqp://flower:{{ rabbitmq_users_password.flower }}@{{ inventory_hostname }}:5671/galaxy_internal?ssl=1" flower_proxy_prefix: /flower - +flower_user: "{{ galaxy_user.name }}" +flower_group: "{{ galaxy_user.group }}" flower_ui_users: - name: admin - password: "{{ vault_flower_user_password}}" + password: "{{ flower_admin_password }}" flower_environment_variables: GALAXY_CONFIG_FILE: "{{ galaxy_config_file }}" -# Telegraf -telegraf_plugins_extra: - listen_galaxy_routes: - plugin: "statsd" - config: - - service_address = ":8125" - - metric_separator = "." - - allowed_pending_messages = 10000 - monitor_galaxy_queue: - plugin: "exec" - config: - - commands = ["/usr/bin/env PGDATABASE=galaxy /usr/local/bin/gxadmin iquery queue-overview --short-tool-id"] - - timeout = "10s" - - data_format = "influx" - - interval = "15s" - -# TIaaS setup -tiaas_dir: /srv/tiaas -tiaas_admin_user: admin -tiaas_admin_pass: changeme - # Proftpd: proftpd_galaxy_auth: yes galaxy_ftp_upload_dir: "{{ galaxy_config.galaxy.ftp_upload_dir }}" @@ -476,15 +460,14 @@ proftpd_display_connect: | Unauthorized access is prohibited proftpd_create_ftp_upload_dir: yes proftpd_options: - - User: galaxy - - Group: galaxy + - User: "{{ galaxy_user.name }}" + - Group: "{{ galaxy_user.group }}" - Port: 21 -proftpd_sql_db: galaxy@/var/run/postgresql -proftpd_sql_user: galaxy +proftpd_sql_db: "{{ galaxy_db_name }}@/var/run/postgresql" +proftpd_sql_user: "{{ galaxy_user.name }}" proftpd_conf_ssl_certificate: /etc/letsencrypt/live/{{ inventory_hostname }}/cert.pem proftpd_conf_ssl_certificate_key: /etc/letsencrypt/live/{{ inventory_hostname }}/privkey.pem proftpd_global_options: - PassivePorts: 56000 60000 proftpd_use_mod_tls_shmcache: false proftpd_tls_options: NoSessionReuseRequired - diff --git a/group_vars/secret.yml b/group_vars/secret.yml index eb3d58a..327f180 100644 --- a/group_vars/secret.yml +++ b/group_vars/secret.yml @@ -1,46 +1,30 @@ $ANSIBLE_VAULT;1.1;AES256 -30303337656261656337666563646337353937343463663462643364653435633864396434373730 -3861376165613462656536633532326331373265663836350a663963613461383734613038653462 -61646663323835363465333536323961613836306564623431303630326665313462633061336634 -6662346165646435300a373938366139356565626434633637616133313530613061363037343439 -38366234393537653534303038366264663336636336663038303564646163653864316235383263 -36613032646261366163313132316531396439393334653833366533353332363734303438653163 -63323464366335666432396634386231636662643661393233393564666135666634623065623832 -30393261666363323337336532656433383364396134616230346162303637363734323938316238 -33393665336562646138613165303562646463623033343631663065343735616536313638303830 -62376462303765346431643333666662333131393236363066376661626139343061303336653338 -34663264633163376230646139343635323439656439313363346565333934343831653430623834 -34663266633436616432383838383963383032393765663764383736366566313864333337393637 -63333366373130653837633465643839653063346262373631333666626538323662616565303363 -63633163353362626662383035643939336465633239643730313162636330613663633564636630 -31643534303934656263623335613366386136346161393835633632613166346635353862633466 -63306166633762623665353934353362656162323835653865626333353462326466376135306264 -39616335343163653366633562333631336364316230336432353763363236303764653937346432 -34366532313631346331393464323633393338626363353637316238353262633933333030326264 -30626665316630353866386232663038333237643231303033636530303361343764356232353134 -39376138336562373233353962666264336630363432396561313665376533663262653765383064 -32653862623966396238633062616130663563326661636137333437653862386564313536643531 -35343838313135363435323665343534343633316635323564633336393633346235366263396138 -31313835623262313661306337326665373666343336633934656162356431363836343131646330 -37313066353261656633613430373538656331653161343866373235646338343338376465396431 -30363031353062646365313066643938663030613264313561316562383432373165333862633766 -37316566643930373464303634396439353963613062393335643466656538663238386634336437 -32343363313434643031653732343661343566343666393032353533666462303765656135343531 -37393130306561313737366331313134343130373162653736653631353835366564356233313165 -30343965643536333462616566333162303135336566643337386636656665343462373533396662 -30633866653633363461343136313038326337616139636230326331323036316661366566656431 -35333835386364353363623337323334303238383264383039336330306635323564353264666365 -62613036346637623631386630643662626164656531376665393965666535663261333939636366 -37313163323935626363613334323939653331616664383061663965376366343563323735646430 -36663934353866323632366638373564333065653434316161376533656365653464333739313766 -38623335373337656261336535393032633932613231336163313033336537313434313336643763 -34353262663265363364626465663532303630363761653463373838356532336432356563343239 -34636436623539376565616165386432656638323964316539626564623433633563616634346564 -65346163323633363335316338663335663735663830653965306364663662616331383739313564 -61336662323534666465373233613933303934343738626466613535383461646163623630373430 -64653561363536366630653831633431613863646361353365316235393963663533636534326466 -31616230393936646635303235656563626531393235636262363063616461653963303632646136 -33326461323861646137616537623162653034656537333261366466356439313963623637346465 -31323938363164656261316538613538643733303439653662646637343964386561396337343533 -39363737653738663435646134653936363737306431323733376163633162393065313137666533 -32653763666264653263376563623866373635656436373364353336323531326432 +64626132343163623330373930356561326465323738616538373763313731343730343262383337 +6531346361343038376438313562623430336138396530320a363866643862333161356436343935 +37366533373035323065633962386435343338616135313834303336633361383864383831653237 +3536383037636636390a303437643233663166633131353038663937646439323035616134356236 +33663830346664323163303863633066393539383338653639356164643034336165613836613866 +31613838666530316635646133343230333465633935333066306235373431353431383035363233 +35626231383765363132343664373631356365353534376639653963386464396536313165656236 +36313933373263356334326633616262353339316563313864613539323530636462383932393330 +32326234666262623263353033306336346235343562303166626236336565656530666339383163 +34633635643535653064366137626562613730333566613434623931313931366562346534333435 +66623338646134343338313764633639346638383539393961656364643065663936663131616339 +65373664343264323039643936623337623430353433636465316461333233363664633863363036 +63636436303334313537353634633064336337326134623837396364383535326530613361626364 +37666666373236363364393735333834336638653162373965303534363738386535653966373730 +30386264356665623538383163613737313831616439643862616365363336356134663838376465 +39623030313936353865333933646366613461666365376334623162653865376432343533663663 +39623365656563356664646633626238356566316136623163303138323235323932623034616331 +33383631393430613165336535333736653938323962336432653638333138326139626566376132 +33363639613130343334666437343235633865396661303433623961643361623065653634366466 +38636566343035306638363161633532643839373534396432343462383565306166623630346432 +62323431643836353738363336346237386132373939303866623837396661363637343563626437 +64343365363134363334376565623366383531393832366562333937353665323135306137303736 +33623763343437336439663137613938316535386366333739633238323863373665623932346632 +34326463613135333336316465623661626461393938336533643038393566333637646462386665 +64393366656130306334366561663230643932353839306330613261303031373739386634346236 +62316230643230326436636164393264623730303163383933316463666231336664393631613435 +66623731373061336261343636623763313039333533663865626634306632656431663963383762 +32306265396561373333653237323534663038613931353565316330386537343262313937313932 +6631 diff --git a/hosts b/hosts index 20f29fa..40d3d3c 100644 --- a/hosts +++ b/hosts @@ -1,9 +1,11 @@ [galaxyservers] -usegalaxy.cz ansible_connection=local ansible_user=debian +#usegalaxy.cz ansible_connection=local ansible_user=debian +#galaxy-re.grid.cesnet.cz ansible_connection=local ansible_user=debian +galaxy-umsa.grid.cesnet.cz ansible_connection=local ansible_user=debian [dbservers:children] galaxyservers [monitoring] -usegalaxy.cz ansible_connection=local ansible_user=debian +galaxy-umsa.grid.cesnet.cz ansible_connection=local ansible_user=debian [sentryservers] -usegalaxy.cz ansible_connection=local ansible_user=debian +galaxy-umsa.grid.cesnet.cz ansible_connection=local ansible_user=debian diff --git a/roles/galaxyproject.nginx/tasks/ssl-common.yml b/roles/galaxyproject.nginx/tasks/ssl-common.yml index 3e83bb5..1128aca 100644 --- a/roles/galaxyproject.nginx/tasks/ssl-common.yml +++ b/roles/galaxyproject.nginx/tasks/ssl-common.yml @@ -13,6 +13,17 @@ - reload nginx - supervisorctl restart nginx +#- name: Disable ssl_protocols in nginx.conf if set +# lineinfile: +# name: "{{ nginx_conf_file }}" +# regexp: '^(\s*ssl_protocols\s.*)' +# backrefs: yes +# line: '#\1 # commented by Ansible' +# backup: yes +# notify: +# - reload nginx +# - supervisorctl restart nginx + - name: Configure server-wide SSL template: src: ssl.conf.j2 diff --git a/roles/galaxyproject.postgresql/defaults/main.yml b/roles/galaxyproject.postgresql/defaults/main.yml index bd7cace..e8e6e46 100644 --- a/roles/galaxyproject.postgresql/defaults/main.yml +++ b/roles/galaxyproject.postgresql/defaults/main.yml @@ -33,7 +33,7 @@ __postgresql_pgdg_bin_dir: "{{ '/usr/pgsql-' ~ (postgresql_version | replace('.' postgresql_backup_command: >- {{ postgresql_backup_local_dir | quote }}/bin/backup.py {{ '--rsync-connect-opts ' ~ (postgresql_backup_rsync_connect_opts | quote) if postgresql_backup_rsync_connect_opts else '' }} - --rsync-backup-opts {{ postgresql_backup_rsync_backup_opts | quote }} + --rsync-backup-opts={{ postgresql_backup_rsync_backup_opts | quote }} --keep {{ postgresql_backup_keep | quote }} {{ '--pg-bin-dir ' ~ __postgresql_pgdg_bin_dir if ansible_os_family == 'RedHat' else '' }} --backup --clean-archive {{ postgresql_backup_dir | quote }} diff --git a/templates/galaxy/config/object_store_conf.xml.j2 b/templates/galaxy/config/object_store_conf.xml.j2 index 290d799..191a30f 100644 --- a/templates/galaxy/config/object_store_conf.xml.j2 +++ b/templates/galaxy/config/object_store_conf.xml.j2 @@ -2,12 +2,9 @@ - - - - - - + + + diff --git a/templates/galaxy/config/oidc_backends_config.xml b/templates/galaxy/config/oidc_backends_config.xml index 75b935d..23bebdb 100644 --- a/templates/galaxy/config/oidc_backends_config.xml +++ b/templates/galaxy/config/oidc_backends_config.xml @@ -1,12 +1,5 @@ - - {{ e_infra_client_id }} - {{ e_infra_client_secret }} - https://{{ inventory_hostname }}/authnz/keycloak/callback - https://login.e-infra.cz/oidc - https://www.e-infra.cz/img/logo.svg - {{ elixir_client_id }} {{ elixir_client_secret }} diff --git a/templates/galaxy/config/sanitize_allowlist.txt b/templates/galaxy/config/sanitize_allowlist.txt new file mode 100644 index 0000000..964e487 --- /dev/null +++ b/templates/galaxy/config/sanitize_allowlist.txt @@ -0,0 +1 @@ +toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc diff --git a/templates/nginx/galaxy.j2 b/templates/nginx/galaxy.j2 index 9009161..1cbc9d6 100644 --- a/templates/nginx/galaxy.j2 +++ b/templates/nginx/galaxy.j2 @@ -15,7 +15,7 @@ server { # Our log files will go to journalctl access_log syslog:server=unix:/dev/log; error_log syslog:server=unix:/dev/log; - # client_body_temp_path /rbd/data/nginx_upload_store; + # client_body_temp_path {{ galaxy_data_prefix }}/nginx_upload_store; client_body_buffer_size 1024m; client_max_body_size 20G; @@ -30,42 +30,6 @@ server { proxy_set_header Upgrade $http_upgrade; } - location /_job_files { - if ($request_method != POST) { - rewrite "" /api/jobs/$arg_job_id/files last; - } - upload_store {{ galaxy_config['galaxy']['nginx_upload_job_files_store'] }}; - # the rate limit might be needed if we have many Pulsar jobs that are writing data back - # we need to limit it because the disc IO can be too large, ideally this happens on a different node - # upload_limit_rate 32k; - upload_store_access user:rw group:rw all:rw; - upload_pass_form_field ""; - upload_set_form_field "__${upload_field_name}_path" "$upload_tmp_path"; - upload_pass_args on; - upload_pass /_upload_job_files_done; - } - - location /_upload_job_files_done { - internal; - rewrite "" /api/jobs/$arg_job_id/files; - } - - location /api/upload/resumable_upload { - # Disable request and response buffering - proxy_request_buffering off; - proxy_buffering off; - proxy_http_version 1.1; - - # Add X-Forwarded-* headers - proxy_set_header X-Forwarded-Host $host; - proxy_set_header X-Forwarded-Proto $scheme; - - proxy_set_header Upgrade $http_upgrade; - proxy_set_header Connection "upgrade"; - client_max_body_size 0; - proxy_pass http://localhost:{{ galaxy_tusd_port }}/files; - } - # Static files can be more efficiently served by Nginx. Why send the # request to Gunicorn which should be spending its time doing more useful # things like serving Galaxy! @@ -102,42 +66,24 @@ server { alias /; } - # Support click-to-run in the GTN-in-Galaxy Webhook - location /training-material/ { - proxy_pass https://training.galaxyproject.org/training-material/; - } - - location ~* /rabbitmq/(.*) { - rewrite ^/rabbitmq/(.*)$ /$1 break; - proxy_pass http://127.0.0.1:15672; - proxy_buffering off; - proxy_set_header Host $http_host; - proxy_set_header X-Real-IP $remote_addr; - proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; - proxy_set_header X-Forwarded-Proto $scheme; - } - - location /flower { - proxy_pass http://localhost:5555; - proxy_set_header Host $host; - proxy_redirect off; - proxy_http_version 1.1; - proxy_set_header Upgrade $http_upgrade; - proxy_set_header Connection "upgrade"; - } - - location /reports/ { - auth_basic galaxy; - auth_basic_user_file /etc/nginx/passwd; - proxy_pass http://{{ galaxy_config.gravity.reports.bind }}:/; - } - - location /grafana/ { - proxy_pass http://127.0.0.1:3000/; - proxy_set_header Host $http_host; - } - - {{ tiaas_nginx_routes }} +# location ~* /rabbitmq/(.*) { +# rewrite ^/rabbitmq/(.*)$ /$1 break; +# proxy_pass http://127.0.0.1:15672; +# proxy_buffering off; +# proxy_set_header Host $http_host; +# proxy_set_header X-Real-IP $remote_addr; +# proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; +# proxy_set_header X-Forwarded-Proto $scheme; +# } + +# location /flower { +# proxy_pass http://localhost:5555; +# proxy_set_header Host $host; +# proxy_redirect off; +# proxy_http_version 1.1; +# proxy_set_header Upgrade $http_upgrade; +# proxy_set_header Connection "upgrade"; +# } }