From 6a339783263b8ff076c5ef6aee0c65c626f1fee5 Mon Sep 17 00:00:00 2001 From: BorisYourich Date: Wed, 5 Jul 2023 11:17:02 +0200 Subject: [PATCH 1/2] Pulsar and OIDC changes --- files/galaxy/config/tpv_rules_local.yml | 71 ++++++++++++++++++- galaxy.yml | 7 ++ group_vars/galaxyservers.yml | 53 ++++++++++++-- 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 | 2 +- 7 files changed, 141 insertions(+), 10 deletions(-) create mode 100644 templates/galaxy/config/object_store_conf.xml.j2 diff --git a/files/galaxy/config/tpv_rules_local.yml b/files/galaxy/config/tpv_rules_local.yml index a5758ba..47df64d 100644 --- a/files/galaxy/config/tpv_rules_local.yml +++ b/files/galaxy/config/tpv_rules_local.yml @@ -38,6 +38,10 @@ tools: # scheduling: # require: # - pulsar + .*/alphafold/.*: + scheduling: + require: + - gpu roles: training.*: @@ -77,15 +81,78 @@ 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-test/files/staging" + persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz-test/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-test/files/staging" + persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz-test/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/galaxy.yml b/galaxy.yml index 3768316..eea2431 100644 --- a/galaxy.yml +++ b/galaxy.yml @@ -41,6 +41,13 @@ - git: repo: 'https://github.com/usegalaxy-eu/libraries-training-repo' dest: /libraries/ + - name: Create the second storage directory + file: + owner: galaxy + group: galaxy + path: /rbd/data2 + state: directory + mode: '0755' roles: - galaxyproject.tusd - usegalaxy_eu.apptainer diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index 6a50044..6d84c26 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: release_23.0 # 7a9ba0c6529d72517c7627422eac16eadff15b46 +galaxy_commit_id: dde02a8 # release_23.0 # 7a9ba0c6529d72517c7627422eac16eadff15b46 galaxy_force_checkout: true miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda" miniconda_version: 4.12.0 @@ -22,7 +22,7 @@ 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://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 @@ -38,7 +38,7 @@ galaxy_job_config: 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 }}" @@ -74,8 +74,8 @@ 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-test/files/staging" + persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz-test/files/persistent" remote_metadata: false rewrite_parameters: true transport: curl @@ -98,6 +98,44 @@ galaxy_job_config: value: "$SCRATCHDIR" - name: TEMP value: "$SCRATCHDIR" + pulsar_gpu: + runner: pulsar_gpu_runner + default_file_action: remote_transfer + transport: curl + dependency_resolution: remote + jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz-test/files/staging" + persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz-test/files/persistent" + remote_metadata: false + rewrite_parameters: true + outputs_to_working_directory: false + singularity_enabled: true + singularity_run_extra_arguments: '--nv' + singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data:ro' + env: + # The cache directory holds the docker containers that get converted + - name: SINGULARITY_CACHEDIR + # value: "/tmp/singularity" + value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" + - name: APPTAINER_CACHEDIR + value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" + # Singularity uses a temporary directory to build the squashfs filesystem + - name: SINGULARITY_TMPDIR + value: "/storage/praha5-elixir/home/galaxyeu/singularity/tmp" + - name: APPTAINER_TMPDIR + value: "/storage/praha5-elixir/home/galaxyeu/singularity/tmp" + # Alphafold specific variables + - name: ALPHAFOLD_DB + value: "/storage/brno11-elixir/projects/alphafold/alphafold.db-2.3.1" + # Default variables + - name: TMPDIR + value: "$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 +159,7 @@ galaxy_job_config: galaxy_config: galaxy: # Main Configuration + 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 +170,7 @@ galaxy_config: - 499542@muni.cz - 325073@mail.muni.cz - demko@cesnet.cz + smtp_server: "https://galaxy-cz.grid.cesnet.cz/:587" allow_user_creation: False database_connection: "postgresql:///{{ galaxy_db_name }}?host=/var/run/postgresql" file_path: /mnt/data/datasets @@ -139,6 +179,7 @@ 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 +290,8 @@ 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 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..65460e1 --- /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..80c1233 100644 --- a/templates/galaxy/config/oidc_backends_config.xml +++ b/templates/galaxy/config/oidc_backends_config.xml @@ -3,7 +3,7 @@ {{ e_infra_client_id }} {{ e_infra_client_secret }} - https://usegalaxy-test.cerit-sc.cz/authnz/keycloak/callback + https://galaxy-cz.grid.cesnet.cz/authnz/keycloak/callback https://login.e-infra.cz/oidc https://www.e-infra.cz/img/logo.svg From 3c7b630e90576967a0cf3261290a5d42ea8b5367 Mon Sep 17 00:00:00 2001 From: BorisYourich Date: Fri, 20 Oct 2023 14:32:46 +0200 Subject: [PATCH 2/2] Welcome page updates --- add_group_users.py | 36 + ansible.cfg | 4 +- eu_tool_list.yaml | 4055 ++++++++++------- files/galaxy/config/tpv_rules_local.yml | 19 +- files/galaxy/e-infra_logo.svg | 290 ++ files/galaxy/elixir_logo.png | Bin 0 -> 17238 bytes files/galaxy/tools/testing.xml | 11 +- files/galaxy/usegalaxy-cz.png | Bin 0 -> 20852 bytes files/galaxy/welcome.html | 38 +- galaxy.yml | 28 +- group_vars/galaxyservers.yml | 43 +- group_vars/secret.yml | 83 +- hosts | 6 +- roles/galaxyproject.nginx/tasks/apt.yml | 10 +- .../galaxy/config/object_store_conf.xml.j2 | 8 +- .../galaxy/config/oidc_backends_config.xml | 9 +- templates/galaxy/config/tool_conf.xml.j2 | 606 +++ templates/nginx/galaxy.j2 | 24 +- 18 files changed, 3599 insertions(+), 1671 deletions(-) create mode 100755 add_group_users.py create mode 100644 files/galaxy/e-infra_logo.svg create mode 100644 files/galaxy/elixir_logo.png create mode 100644 files/galaxy/usegalaxy-cz.png create mode 100644 templates/galaxy/config/tool_conf.xml.j2 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]) diff --git a/ansible.cfg b/ansible.cfg index bc40777..2c1e546 100644 --- a/ansible.cfg +++ b/ansible.cfg @@ -4,11 +4,11 @@ inventory = hosts retry_files_enabled = false vault_password_file = .vault-password.txt gather_subset=!hardware -no_log = True +# no_log = True # Show diffs of changes [diff] -always = False +always = True [ssh_connection] pipelining = true diff --git a/eu_tool_list.yaml b/eu_tool_list.yaml index 7015f16..236ed07 100644 --- a/eu_tool_list.yaml +++ b/eu_tool_list.yaml @@ -14,9 +14,8 @@ tools: - name: sra_tools owner: iuc revisions: + - 734abc7ac21d - f5ea3ce9b9b0 - - 83c7d564b128 - - 69ebb7f46e45 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download @@ -28,14 +27,14 @@ 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 + - f64b3c1a80a6 + tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp @@ -160,19 +159,19 @@ tools: - name: ega_download_client owner: iuc revisions: - - 9564758e8638 + - 7d87a9d58aa1 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_datasets owner: iuc revisions: - - 1e188c9610c3 + - 75acf92c8fd5 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pysradb_search owner: iuc revisions: - - f63cf0adfd87 + - b91e1e70f3a1 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 +222,6 @@ tools: - 3ddd99c7efee tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu -- name: filter_tabular - owner: iuc - revisions: - - 4d5aae46f850 - tool_panel_section_label: Text Manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: dna_filtering owner: devteam revisions: @@ -286,7 +279,7 @@ 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 @@ -305,7 +298,7 @@ tools: - name: query_tabular owner: iuc revisions: - - cf34c344508d + - 3a6b78c39dca tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_chromosome_names @@ -320,6 +313,12 @@ tools: - b722161a845a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu +- name: filter_tabular + owner: iuc + revisions: + - 557ec8d7087d + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu - name: jq owner: iuc revisions: @@ -443,7 +442,7 @@ tools: - name: add_value owner: devteam revisions: - - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -462,7 +461,7 @@ tools: owner: bgruening revisions: - f71fd828c126 - tool_panel_section_label: Convert Formats + tool_panel_section_label: Import/manipulate sc data tool_shed_url: toolshed.g2.bx.psu.edu - name: glimmer_glimmer_to_gff owner: bgruening @@ -470,11 +469,11 @@ tools: - 891b330ffd94 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: gffcompare - owner: iuc +- name: agat + owner: bgruening revisions: - - 0f710191a66d - tool_panel_section_label: BED + - 6d8444408ff1 + tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_by_fasta_ids owner: galaxyp @@ -512,25 +511,43 @@ tools: - 2429b413d90a tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu +- name: gffcompare + owner: iuc + revisions: + - 0f710191a66d + tool_panel_section_label: Filter and Sort + tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - ac092723240d + - 374cb875d38a tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_reverse owner: iuc revisions: - - f198773344e4 + - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_ops owner: iuc revisions: + - 4c07ddedc198 - 2f3c6f2dcf39 - - 746e8e4bf929 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_gff_split + owner: cpt + revisions: + - 8bd03ba8510a + tool_panel_section_label: Convert Formats + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_gbk_to_5col + owner: cpt + revisions: + - 1bdd481d5c25 + tool_panel_section_label: Convert Formats + tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta owner: devteam revisions: @@ -564,14 +581,14 @@ tools: - name: msconvert owner: galaxyp revisions: - - 6153e8ada1ee - dd4ba10d0c45 + - 6153e8ada1ee tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: interval2maf owner: iuc revisions: - - 1080e07a2233 + - 7adddc6015c1 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: crossmap_wig @@ -643,7 +660,7 @@ tools: - name: biom_convert owner: iuc revisions: - - e525f9ffb9ac + - e177a8ea0bf1 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: resize_coordinate_window @@ -682,6 +699,18 @@ tools: - eb09d7e6d727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_gff_to_gbk + owner: cpt + revisions: + - 35a6c466e270 + tool_panel_section_label: Convert Formats + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_gbk_to_gff + owner: cpt + revisions: + - bb6332a85aa6 + tool_panel_section_label: Convert Formats + tool_shed_url: toolshed.g2.bx.psu.edu - name: intermine_galaxy_exchange owner: iuc revisions: @@ -754,6 +783,18 @@ tools: - 4a9ac1df3278 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_convert_mga + owner: cpt + revisions: + - 1bf722ba06e3 + tool_panel_section_label: Convert Formats + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_fix_aragorn + owner: cpt + revisions: + - 733cb0807083 + tool_panel_section_label: Convert Formats + tool_shed_url: toolshed.g2.bx.psu.edu - name: short_reads_trim_seq owner: devteam revisions: @@ -865,61 +906,61 @@ tools: - name: fastx_renamer owner: devteam revisions: - - b29d37ca9e41 + - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - 6027ef51ef91 + - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - - 61b4cedc8934 + - 73194cdd4f57 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: - - e282bc27be9a + - 77b41c89d856 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - 59003d0543cd + - cc0fd298cc17 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_boxplot owner: devteam revisions: - - 7cf5b1d072b5 + - 867ab348287d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: - - 54053ea6c77e + - 045f0e1043f7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_filter owner: devteam revisions: - - ce9cd02d5b88 + - 64e9a6afdd0c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: - - 859422bcb689 + - 516b97a23d7e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: - - ec0b5076173a + - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic @@ -931,7 +972,7 @@ tools: - name: fastx_collapser owner: devteam revisions: - - 7ce1891db6f5 + - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -970,31 +1011,19 @@ tools: - 0a7799698fe5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: fasta_regex_finder - owner: mbernt - revisions: - - 9a811adb714f - tool_panel_section_label: FASTA/FASTQ - tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter owner: devteam revisions: - - d5e9e83cd3d8 + - 529bccd5e4a1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate owner: iuc revisions: - - a03dead1bede - 2485637fe656 + - a03dead1bede tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastqc - owner: devteam - revisions: - - 3d0c7bdf12f5 - tool_panel_section_label: FASTA/FASTQ - tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: @@ -1022,8 +1051,8 @@ tools: - name: seqtk owner: iuc revisions: - - 3da72230c066 - a09586d5149a + - 3da72230c066 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group @@ -1065,25 +1094,25 @@ tools: - name: fastx_clipper owner: devteam revisions: - - cb1e251cac37 + - 90858c306551 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt owner: lparsons revisions: - - 135b80fb1ac2 + - 8c0175e03cee tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - ad116ae3f4d9 + - b6b54ba71bd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 4bedca26c133 + - 0b7ec11b3c7c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: bctools_extract_crosslinked_nucleotides @@ -1104,6 +1133,12 @@ tools: - 9839a3fe72f7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastqc + owner: devteam + revisions: + - 5ec9f6bceaee + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu - name: bctools_convert_to_binary_barcode owner: iuc revisions: @@ -1254,6 +1289,30 @@ tools: - 6510652376b1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu +- name: fasta_regex_finder + owner: mbernt + revisions: + - 9a811adb714f + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bbtools_bbduk + owner: iuc + revisions: + - 159b04e36791 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bbtools_bbmerge + owner: iuc + revisions: + - c05232655d00 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_fasta_remove_id + owner: cpt + revisions: + - 78222649a59a + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: @@ -1272,12 +1331,6 @@ tools: - 7a821cd57b43 tool_panel_section_label: Quality Control 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: pileup_interval owner: devteam revisions: @@ -1371,7 +1424,7 @@ tools: - 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 +1490,7 @@ 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 +1499,28 @@ tools: - 2e957d4c4b95 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: bamtools_split_mapped - owner: iuc +- name: bamtools_filter + owner: devteam revisions: - - 6dbef7ea2253 + - 108db6635177 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: samtools_calmd + owner: devteam + revisions: + - 92ec40abcdcf + 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: bamhash + owner: bgruening + revisions: + - 63f6f42d112b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_paired @@ -1464,28 +1535,22 @@ tools: - 9b520009db81 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: bamtools_split_tag +- name: bamtools_split_mapped owner: iuc revisions: - - e30af4e78cd3 - tool_panel_section_label: SAM/BAM - tool_shed_url: toolshed.g2.bx.psu.edu -- name: samtools_calmd - owner: devteam - revisions: - - 92ec40abcdcf + - 6dbef7ea2253 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: samtools_phase - owner: devteam +- name: bamtools_split_tag + owner: iuc revisions: - - 1e5880498f52 + - e30af4e78cd3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: bamhash - owner: bgruening +- name: varscan + owner: fcaramia revisions: - - 63f6f42d112b + - 51969e284317 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamutil_diff @@ -1506,14 +1571,33 @@ tools: - 21ddefab2e4f 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: mosdepth + owner: iuc + revisions: + - 69f93450c57d + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu - name: bedtools owner: iuc revisions: - - 589e7e57fd6d - - dde39ba9c031 - - 07e8b80f278c - b8348686a0b9 - ce3c7f062223 + - 07e8b80f278c + - a1a923cd89e8 + - dde39ba9c031 + - 589e7e57fd6d + tool_panel_section_label: BED + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bedops_sortbed + owner: iuc + revisions: + - baeee32175e8 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter @@ -1684,6 +1768,78 @@ tools: - 71e19ddf52f5 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcf2tsv + owner: anton + revisions: + - fc3c4fc09e28 + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfgeno2haplo + owner: anton + revisions: + - a6cd013745fd + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfallelicprimitives + owner: anton + revisions: + - 239da20770dc + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfannotate + owner: anton + revisions: + - 027fe0a0076e + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfannotategenotypes + owner: anton + revisions: + - 846a4449a50a + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfbedintersect + owner: anton + revisions: + - 7e8a201b4c1c + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfgenotypes + owner: anton + revisions: + - 6c636da8765c + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfcheck + owner: anton + revisions: + - 42e3f0702878 + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfcombine + owner: anton + revisions: + - c079222f1e38 + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfcommonsamples + owner: anton + revisions: + - 6a1a90ea160f + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfdistance + owner: anton + revisions: + - de3bbf60d086 + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfbreakcreatemulti + owner: anton + revisions: + - c0387293312e + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_compare owner: devteam revisions: @@ -1711,7 +1867,7 @@ tools: - name: medaka_variant owner: iuc revisions: - - ec699520444c + - eb746fa6f514 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: flair_correct @@ -1741,13 +1897,13 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - 79e9a869f40e + - fc8804320156 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - 682d1e2c8be4 + - 18505fe2bdb1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_db @@ -1759,7 +1915,7 @@ tools: - name: nanoplot owner: iuc revisions: - - a3c4fe6f49ab + - 0f1c34698076 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: ont_fast5_api_multi_to_single_fast5 @@ -1915,7 +2071,7 @@ tools: - name: pycoqc owner: iuc revisions: - - 3a2f2e24c37e + - dc1500f42073 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: clair3 @@ -1990,28 +2146,34 @@ tools: - 642d73815dd1 tool_panel_section_label: Fetch Sequences / Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: gffcompare - owner: iuc +- name: braker3 + owner: genouest revisions: - - f99dd58de04f + - bd103884a09c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: cpat - owner: bgruening +- name: cpt_phageqc_annotations + owner: cpt revisions: - - 8e9e228c54c4 + - c3140b08d703 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: goseq - owner: iuc +- name: cpt_gff_extract_seq + owner: cpt revisions: - - 602de62d995b + - ab40380424c9 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_intron_detection + owner: cpt + revisions: + - 0a98d5259ef0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - bb935709506a + - 94170eee0ad8 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: optitype @@ -2035,7 +2197,7 @@ tools: - name: tbprofiler owner: iuc revisions: - - 45083d070fb8 + - 2c68b0c38785 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: hmmer_nhmmer @@ -2095,7 +2257,7 @@ tools: - name: annotatemyids owner: iuc revisions: - - fe3ca740a485 + - cd2480f35935 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -2119,7 +2281,7 @@ tools: - name: mitos owner: iuc revisions: - - f20804c311de + - c7553ba39670 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -2155,13 +2317,13 @@ tools: - 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 @@ -2290,6 +2452,12 @@ tools: - ce0c9fe32e04 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu +- name: goseq + owner: iuc + revisions: + - 602de62d995b + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu - name: snap_training owner: iuc revisions: @@ -2308,12 +2476,6 @@ tools: - 17eb1e0d711f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: sortmerna - owner: rnateam - revisions: - - eb35257d2e29 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: spaln owner: iuc revisions: @@ -2344,36 +2506,12 @@ tools: - 4db310b7e37c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: integron_finder - owner: iuc - revisions: - - 1ae00120dd24 - tool_panel_section_label: Annotation - tool_shed_url: toolshed.g2.bx.psu.edu - name: tmhmm_and_signalp owner: peterjc revisions: - 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: @@ -2429,6 +2567,12 @@ tools: - 96e6283e4745 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu +- name: sortmerna + owner: rnateam + revisions: + - eb35257d2e29 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu - name: probmetab owner: mmonsoor revisions: @@ -2465,19 +2609,49 @@ tools: - 42d20ff5da1b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: blast2go - owner: peterjc +- name: cpt_lipory + owner: cpt revisions: - - 8664c4c94764 + - b79df4966ebb tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: hmmer_alimask - owner: iuc +- name: cpt_gbk_renumber + owner: cpt revisions: - - 80c713789d13 + - 8cac332dbc77 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: hmmer_hmmalign +- name: cpt_genome_editor + owner: cpt + revisions: + - 78ce8a1a8fd1 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_annotation_table + owner: cpt + revisions: + - 6998c2570145 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_gff_rebase + owner: cpt + revisions: + - 4f4b413056f6 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_require_shine + owner: cpt + revisions: + - a6dc48930318 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: hmmer_alimask + owner: iuc + revisions: + - 80c713789d13 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: hmmer_hmmalign owner: iuc revisions: - 24fa8e890f08 @@ -2522,8 +2696,8 @@ tools: - name: dgidb_annotator owner: devteam revisions: - - c5bb987015c5 - 792f3cb0eff4 + - c5bb987015c5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: hhsearch @@ -2559,7 +2733,7 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - ee4a90760848 + - 32f14a2723ec tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: lorikeet_spoligotype @@ -2577,37 +2751,37 @@ 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 revisions: - - 3f987772e283 + - ba6d2c32f797 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: homer_scanmotifgenomewide owner: iuc revisions: - - db456c398880 + - f15794662a69 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: homer_annotatepeaks owner: iuc revisions: - - 35dc2f57d755 + - dcd291aeb8a9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: homer_findmotifsgenome owner: iuc revisions: - - a8f207b43f64 + - 081139509124 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: homer_gtf_to_annotations owner: iuc revisions: - - 396cf2c12173 + - df55927535ed tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: hamronize_tool @@ -2625,31 +2799,37 @@ tools: - name: funannotate_clean owner: iuc revisions: - - a230ea445788 + - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - b3cf4684e9c7 + - 52af33194019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 2bba2ff070d9 + - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 563a19373357 + - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_annotate owner: iuc revisions: - - 14f588312c56 + - 582fd74dc2a1 + 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: interproscan @@ -2679,7 +2859,7 @@ tools: - name: miniprot owner: iuc revisions: - - ce04c239454b + - 52bdc302299b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: netboxr @@ -2691,13 +2871,13 @@ tools: - name: plasmidfinder owner: iuc revisions: - - e23b96d79dc0 + - 7075b7a5441b 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 @@ -2706,12 +2886,132 @@ tools: - 18a46265455b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu +- name: integron_finder + owner: iuc + revisions: + - 4768f7f8e93f + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu - name: edta owner: bgruening revisions: - f1a157358d4d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu +- name: bakta + owner: iuc + revisions: + - 728dacaf08a9 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpat + owner: bgruening + revisions: + - 8e9e228c54c4 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: gffcompare + owner: iuc + revisions: + - f99dd58de04f 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cpt_convert_glimmer + owner: cpt + revisions: + - faff58a642fb + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: agat + owner: bgruening + revisions: + - e009d8260be2 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: helixer + owner: genouest + revisions: + - 7bc75dd0f782 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw owner: devteam revisions: @@ -2838,76 +3138,52 @@ tools: - 7807800a3d03 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: nextdenovo - owner: bgruening - revisions: - - 733eab97b979 - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: blobtoolkit - owner: bgruening +- name: shovill + owner: iuc revisions: - - 7d9ee8cd14b8 + - ee17a294d3a3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm owner: bgruening revisions: - - c388a21dcbf1 - 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toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - 59bd28f6265d + - cb1e3db43020 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 05bd7504fdb2 + - 2628f6790eda tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 5732f959936a + - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -2988,16 +3264,10 @@ tools: - 03de4e0f84c2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: shovill - owner: iuc - revisions: - - ad80238462c1 - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - e100a765370e + - 936f0b5e7fcc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -3015,7 +3285,7 @@ tools: - name: quast owner: iuc revisions: - - 3061c8b029e5 + - 72472698a2df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: miniasm @@ -3027,7 +3297,7 @@ tools: - name: abyss owner: iuc revisions: - - 8f1b150a2487 + - a929ce596a34 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler @@ -3135,7 +3405,7 @@ tools: - name: merqury owner: iuc revisions: - - f8113c25bc6b + - 09c589057ee8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope @@ -3150,16 +3420,22 @@ tools: - dfb8a4497339 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu +- 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 + - 321347bd0494 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitohifi owner: bgruening revisions: - - f6065bc6e428 + - 99ddbf037d98 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven @@ -3192,12 +3468,6 @@ tools: - d5fb354f745d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: cactus_cactus - owner: galaxy-australia - revisions: - - 9baa871cb1d1 - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: @@ -3243,7 +3513,7 @@ tools: - name: yahs owner: iuc revisions: - - 39495e107274 + - 425e63adcc5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet @@ -3261,19 +3531,20 @@ tools: - name: smudgeplot owner: galaxy-australia revisions: - - 24e471d13fe9 + - 5a0ddb4dc3a4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapog owner: iuc revisions: - - c61bc8bb5f1e + - 7d56a813fd24 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 @@ -3282,10 +3553,22 @@ tools: - 1f9f2edc8cf4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu +- name: cactus_cactus + owner: galaxy-australia + revisions: + - 94b8c6013083 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cactus_export + owner: galaxy-australia + revisions: + - 3ff17bad4006 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu - name: instagraal owner: bgruening revisions: - - 8d5b13b571fd + - d1be552c6034 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: necat @@ -3300,17 +3583,46 @@ tools: - ef4b5ce71745 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: megablast_xml_parser - owner: devteam +- name: hifiasm_meta + owner: galaxy-australia revisions: - - fbff957a3655 - tool_panel_section_label: Mapping + - fa35f1106d3e + tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: bwa +- name: blobtoolkit + owner: bgruening + revisions: + - 53dd00a4ab68 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: nextdenovo + owner: bgruening + revisions: + - 733eab97b979 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: aligned_to_consensus + owner: ecology + revisions: + - 0ccbe1c20fc3 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: verkko + owner: iuc + revisions: + - cf54dafa0403 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: rnaquast + owner: iuc + revisions: + - f89e3c318453 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: megablast_xml_parser owner: devteam revisions: - - 64f11cf59c6e - - e188dc7a68e6 + - fbff957a3655 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: megablast_wrapper @@ -3328,7 +3640,7 @@ tools: - name: lastz owner: devteam revisions: - - 3e1ea2facca6 + - 37b497aa133f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -3340,7 +3652,7 @@ tools: - name: minimap2 owner: iuc revisions: - - 11a0d50a54e6 + - be1d967337e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -3352,19 +3664,18 @@ tools: - name: rna_starsolo owner: iuc revisions: - - 79b885ce78d7 + - 5ef7ec16b04f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar owner: iuc revisions: - - 980d2a2e1180 + - 79de45b5069b tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bismark owner: bgruening revisions: - - 9d02cd7883ad - 0b656f8c5637 - ff6ee551b153 tool_panel_section_label: Mapping @@ -3405,6 +3716,13 @@ tools: - 190175f4e143 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu +- name: bwa + owner: devteam + revisions: + - e188dc7a68e6 + - 64f11cf59c6e + tool_panel_section_label: Mapping + tool_shed_url: toolshed.g2.bx.psu.edu - name: tophat2 owner: devteam revisions: @@ -3432,220 +3750,112 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - b4a22d90cce9 + - bfaa0d22c2e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmap owner: iuc revisions: - - 858a65b52cf9 + - 517464809c33 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: ucsc_fatovcf +- name: strelka_germline owner: iuc revisions: - - 78df8fc2b3ab + - 19481653a22f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_stats +- name: sansa_annotate owner: iuc revisions: - - a2f8dc22d7c0 + - b1ca9fce4749 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_roh +- name: strelka_somatic owner: iuc revisions: - - bdc67eeb0bc9 + - edbdbc64b397 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_reheader +- name: delly_filter owner: iuc revisions: - - 8057cf55fa41 + - 74f9f312c713 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_query +- name: delly_merge owner: iuc revisions: - - a850902cac64 + - 6c44bbc0eaa5 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_plugin_setgt +- name: delly_call owner: iuc revisions: - - 262bba5b90ef + - c34eab9d5134 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_plugin_frameshifts +- name: delly_lr owner: iuc revisions: - - 399b40b2bcab + - 97f649646cc1 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_filter +- name: bcftools_consensus owner: iuc revisions: - - 656a916779fe + - 147de996e34f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_csq +- name: delly_classify owner: iuc revisions: - - f01b2c9506b9 + - df4300f300e4 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_convert_to_vcf +- name: delly_cnv owner: iuc revisions: - - 4935320a59a8 + - 8ad49c4272ea tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_convert_from_vcf +- name: vcfanno owner: iuc revisions: - - cacc9970727a + - fb20fa735dfe tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_annotate +- name: jasminesv owner: iuc revisions: - - 3f62d4939d54 + - 2b62154e39c8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_call +- name: irissv owner: iuc revisions: - - f0d44631365f + - b4b6b660293a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_consensus +- name: snpfreqplot owner: iuc revisions: - - 147de996e34f + - 3d0adeee3f2b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: varscan_somatic +- name: variant_analyzer 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 - owner: iuc - revisions: - - 9f8dbbbc0267 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: strelka_germline - owner: iuc - revisions: - - 19481653a22f - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: sansa_annotate - owner: iuc - 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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 - owner: iuc - revisions: - - 8ad49c4272ea - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: vcfanno - owner: iuc - revisions: - - fb20fa735dfe - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: jasminesv - owner: iuc - revisions: - - 2b62154e39c8 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: irissv - owner: iuc - revisions: - - 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 + - 3f1dbd2c59bf tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: + - 09d6806c609e + - 2b3e65a4252f - b04635ebfab0 - 5fab4f81391d - - 2b3e65a4252f - - 09d6806c609e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lumpy_sv @@ -3681,7 +3891,7 @@ tools: - name: artic_minion owner: iuc revisions: - - 6f52ebc01098 + - 468b90c41cde tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cutesv @@ -3924,12 +4134,30 @@ tools: - 6ea73d6151ec 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_norm owner: iuc revisions: - ebb2e12a6de1 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_plugin_frameshifts + owner: iuc + revisions: + - 399b40b2bcab + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_color_chrs owner: iuc revisions: @@ -3975,75 +4203,75 @@ tools: - name: snpeff owner: iuc revisions: - - e8adfc4c0a6b - 5c7b70713fb5 - 5b80f544c67f + - e8adfc4c0a6b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: basil +- name: varscan_somatic owner: iuc revisions: - - e6ef29001647 + - cf8ffc79db67 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_gtcheck +- name: basil owner: iuc revisions: - - 3eac729e66c9 + - e6ef29001647 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_isec +- name: bcftools owner: iuc revisions: - - 63aabc920911 + - bdd0cb7fbedf tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_mpileup +- name: vt_variant_tools owner: iuc revisions: - - 03191140c66a + - 6e073fc99d9c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_plugin_split_vep - owner: iuc +- name: naive_variant_caller + owner: blankenberg revisions: - - d55feecb6dc1 + - aff38ea879f1 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_view +- name: snpsift_genesets owner: iuc revisions: - - abc3ced31cd1 + - d12a810c837e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools +- name: snpsift_dbnsfp owner: iuc revisions: - - bdd0cb7fbedf + - 4e21e4f2bc48 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: vt_variant_tools +- name: snpsift_dbnsfp_generic owner: iuc revisions: - - 6e073fc99d9c + - a7cbaf3beadd tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpsift_genesets +- name: varscan_copynumber owner: iuc revisions: - - d12a810c837e + - 9f8dbbbc0267 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpsift_dbnsfp - owner: iuc +- name: varscan_version_2 + owner: devteam revisions: - - 4e21e4f2bc48 + - bc1e0cd41241 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpsift_dbnsfp_generic +- name: varscan_mpileup owner: iuc revisions: - - a7cbaf3beadd + - db94eadb92c1 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snpeff_cds_report @@ -4058,6 +4286,12 @@ tools: - 80eff5812b2a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu +- name: bcftools_plugin_split_vep + owner: iuc + revisions: + - d55feecb6dc1 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu - name: allele_counts owner: nick revisions: @@ -4070,118 +4304,328 @@ tools: - 84f70ce0b830 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: beagle +- name: bcftools_mpileup owner: iuc revisions: - - 553b27c30eb8 + - 03191140c66a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: deepvariant +- name: bcftools_view owner: iuc revisions: - - 98fe794d2ec0 + - abc3ced31cd1 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: king +- name: bcftools_stats owner: iuc revisions: - - 1932808c6fab + - a2f8dc22d7c0 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 owner: iuc revisions: - - 0d18a3ba2d1c + - 3eac729e66c9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: vcf2maf +- name: bcftools_filter owner: iuc revisions: - - e8510e04a86a + - 656a916779fe tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: crispr_studio +- name: bcftools_convert_to_vcf owner: iuc revisions: - - 7346619ad005 - tool_panel_section_label: Genome editing + - 4935320a59a8 + tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: mageck_test +- name: bcftools_convert_from_vcf owner: iuc revisions: - - 688a8eccea71 - tool_panel_section_label: Genome editing + - cacc9970727a + tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: mageck_mle +- name: bcftools_annotate owner: iuc revisions: - - b36c85e37a48 - tool_panel_section_label: Genome editing + - 3f62d4939d54 + tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: mageck_gsea +- name: beagle owner: iuc revisions: - - d46e36492bff - tool_panel_section_label: Genome editing + - f75bf16ac901 + tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: mageck_count +- name: deepvariant owner: iuc revisions: - - 3edbd1ff5602 - tool_panel_section_label: Genome editing + - 918c8b94c8d8 + tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: mageck_pathway +- name: king owner: iuc revisions: - - 9744e1124d0f - tool_panel_section_label: Genome editing + - 1932808c6fab + tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: sonneityping +- name: artic_guppyplex owner: iuc revisions: - - db4fe7172114 - tool_panel_section_label: Genome editing + - 00e20a06ff1e + tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: amplican +- name: pharmcat + owner: bgruening + revisions: + - 891283e0ee89 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bbtools_callvariants owner: iuc revisions: - - 8c1bba8d544a + - ee407fae3ccd + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ensembl_vep + owner: iuc + revisions: + - fdbd97ff825e + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: breseq + owner: iuc + revisions: + - 0d18a3ba2d1c + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcf2maf + owner: iuc + revisions: + - e8510e04a86a + 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: ucsc_fatovcf + owner: iuc + revisions: + - d9965e143053 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_access + owner: iuc + revisions: + - 9f18bcf53f92 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_antitarget + owner: iuc + revisions: + - b52fa1df3bc4 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_autobin + owner: iuc + revisions: + - 94e1d19c8190 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_batch + owner: iuc + revisions: + - 4653aeb60243 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_call + owner: iuc + revisions: + - 0a5e2fc51dfb + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_coverage + owner: iuc + revisions: + - 5602cbf1153b + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_diagram + owner: iuc + revisions: + - 697c61206f5f + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_fix + owner: iuc + revisions: + - dc0fb5f07231 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_heatmap + owner: iuc + revisions: + - d8c45afa221c + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_reference + owner: iuc + revisions: + - 0c3db8ec44b0 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_scatter + owner: iuc + revisions: + - 3323a7867128 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_segment + owner: iuc + revisions: + - c4a22d0fdba5 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_target + owner: iuc + revisions: + - 876630eb0680 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: smgu_frameshift_deletions_checks + owner: iuc + revisions: + - e8971ca74398 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: manta + owner: artbio + revisions: + - cb5691381acb + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: beacon2_csv2xlsx + owner: iuc + revisions: + - ba4ed464f8b6 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: beacon2_pxf2bff + owner: iuc + revisions: + - 30605b5fc43f + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: beacon2_vcf2bff + owner: iuc + revisions: + - 0a757835a745 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_breaks + owner: iuc + revisions: + - ef9a50eb20ce + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_genemetrics + owner: iuc + revisions: + - 2b53415d4f3c + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_segmetrics + owner: iuc + revisions: + - d9cb65e1f756 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cnvkit_sex + owner: iuc + revisions: + - 3316bd294f6f + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: crispr_studio + owner: iuc + revisions: + - 7346619ad005 tool_panel_section_label: Genome editing tool_shed_url: toolshed.g2.bx.psu.edu -- name: isoformswitchanalyzer +- name: mageck_test owner: iuc revisions: - - f3fefb6d8254 - tool_panel_section_label: RNA-Seq + - 688a8eccea71 + tool_panel_section_label: Genome editing tool_shed_url: toolshed.g2.bx.psu.edu -- name: cherri_train +- name: mageck_mle owner: iuc revisions: - - a30b9df1775a + - b36c85e37a48 + tool_panel_section_label: Genome editing + tool_shed_url: toolshed.g2.bx.psu.edu +- name: mageck_gsea + owner: iuc + revisions: + - d46e36492bff + tool_panel_section_label: Genome editing + tool_shed_url: toolshed.g2.bx.psu.edu +- name: mageck_count + owner: iuc + revisions: + - 3edbd1ff5602 + tool_panel_section_label: Genome editing + tool_shed_url: toolshed.g2.bx.psu.edu +- name: mageck_pathway + owner: iuc + revisions: + - 9744e1124d0f + tool_panel_section_label: Genome editing + tool_shed_url: toolshed.g2.bx.psu.edu +- name: sonneityping + owner: iuc + revisions: + - db4fe7172114 + tool_panel_section_label: Genome editing + tool_shed_url: toolshed.g2.bx.psu.edu +- name: amplican + owner: iuc + revisions: + - 8c1bba8d544a + tool_panel_section_label: Genome editing + tool_shed_url: toolshed.g2.bx.psu.edu +- name: edger + owner: iuc + revisions: + - 070900306913 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_transcripts_via_tracking @@ -4220,16 +4664,10 @@ tools: - f648e5180e40 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu -- name: rnaquast - owner: iuc - revisions: - - 96f74538896e - tool_panel_section_label: RNA Analysis - tool_shed_url: toolshed.g2.bx.psu.edu - name: ruvseq owner: iuc revisions: - - d1f7fa5bb3cb + - 3a083c78896e tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -4241,7 +4679,7 @@ tools: - name: featurecounts owner: iuc revisions: - - 38b6d12edc68 + - f9d49f5cb597 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: migmap @@ -4254,12 +4692,12 @@ tools: owner: iuc revisions: - a3b3ec00bf8f - tool_panel_section_label: RNA Analysis + tool_panel_section_label: Import/manipulate sc data tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - - 56242ff81c84 + - fab6ff46e019 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: tetoolkit_tetranscripts @@ -4337,13 +4775,13 @@ tools: - name: salmon owner: bgruening revisions: - - ebab418107f5 + - 15cd64d7c58b tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - 8fe98f7094de + - 9a882d108833 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -4355,13 +4793,13 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - c2b82a94493e + - 2fb4ee002432 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity owner: iuc revisions: - - d2bc35f3d1c5 + - 8f1c3df4dd49 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: srnapipe @@ -4410,43 +4848,37 @@ tools: - name: trinity_super_transcripts owner: iuc revisions: - - bdede464821e + - 5c1fc038df6b tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - bcc5f03f1900 + - ba3720d7e68b tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - - be3f26533209 + - 870ac06dff8e tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d + - a35cba31d904 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - - eafea3083352 - tool_panel_section_label: RNA Analysis - tool_shed_url: toolshed.g2.bx.psu.edu -- name: sortmerna - owner: rnateam - revisions: - - 1eafcc450052 + - 24e94d84adc9 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: salmonquantmerge owner: bgruening revisions: - - ee72e302b6a3 + - dba18bf7528f tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: glassgo @@ -4464,19 +4896,13 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 87c11c05d238 + - ce5d418183c5 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - c971db6f0fe5 - tool_panel_section_label: RNA Analysis - tool_shed_url: toolshed.g2.bx.psu.edu -- name: edger - owner: iuc - revisions: - - f2843df56434 + - 4f9c4e6566e5 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: crosscontamination_barcode_filter @@ -4485,12 +4911,6 @@ tools: - 5ade5cf200da tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu -- name: cherri_eval - owner: iuc - revisions: - - cef4148ac5f2 - tool_panel_section_label: RNA Analysis - tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: @@ -4500,8 +4920,7 @@ tools: - name: dexseq owner: iuc revisions: - - 2872c633f07e - - b47c006d90c5 + - df929f257179 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -4651,7 +5070,7 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - 964b7efe2639 + - 7c7fbf13aadd tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -4675,8 +5094,7 @@ tools: - name: rseqc owner: nilesh revisions: - - 5968573462fa - - 2e6190c29c54 + - 473382134e56 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: sshmm @@ -4973,6 +5391,12 @@ tools: - 14267d364365 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu +- name: rnaquast + owner: iuc + revisions: + - 96f74538896e + tool_panel_section_label: RNA Analysis + tool_shed_url: toolshed.g2.bx.psu.edu - name: genomic_super_signature owner: iuc revisions: @@ -4988,19 +5412,19 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 765e685641ce + - 31f8063eedea tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - acbda5dc6955 + - 32e542c2a773 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - f6b8b38636a4 + - 3d61a698e5e1 tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: circexplorer2 @@ -5027,12 +5451,54 @@ tools: - 3f9ff31c88bb tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu +- name: cherri_train + owner: iuc + revisions: + - a30b9df1775a + tool_panel_section_label: RNA Analysis + tool_shed_url: toolshed.g2.bx.psu.edu - name: mirnature owner: iuc revisions: - dd2f87ccbd2c tool_panel_section_label: RNA Analysis tool_shed_url: toolshed.g2.bx.psu.edu +- name: cherri_eval + owner: iuc + revisions: + - cef4148ac5f2 + tool_panel_section_label: RNA Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: isoformswitchanalyzer + owner: iuc + revisions: + - b3f292d9f35d + tool_panel_section_label: RNA Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: sleuth + owner: iuc + revisions: + - d6b5fc94062c + tool_panel_section_label: RNA Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: trinity_stats + owner: iuc + revisions: + - b2ce45417d9e + tool_panel_section_label: RNA Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cmsearch_deoverlap + owner: rnateam + revisions: + - 54b16c794341 + tool_panel_section_label: RNA Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: psiclass + owner: iuc + revisions: + - 1b690aa060f6 + tool_panel_section_label: RNA Analysis + tool_shed_url: toolshed.g2.bx.psu.edu - name: macs owner: devteam revisions: @@ -5072,7 +5538,7 @@ tools: - name: peakachu owner: rnateam revisions: - - 886f5adba83d + - 940b1d632f4d tool_panel_section_label: Peak Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: zerone @@ -5132,8 +5598,8 @@ tools: - name: ewastools owner: kpbioteam revisions: - - 369fef559cfc - fef50103f6b3 + - 369fef559cfc tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -5145,7 +5611,7 @@ tools: - name: bwameth owner: iuc revisions: - - 62f5fab76dfb + - d82648ad25a3 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pileometh @@ -5157,31 +5623,31 @@ tools: - name: hicup_truncater owner: bgruening revisions: - - 17f80a8600ac + - cc413be789ea tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hicup_hicup owner: bgruening revisions: - - bd1594d55a38 + - 68fb19094f84 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hicup_filter owner: bgruening revisions: - - a7bbbf32da62 + - 2d4a34c00c67 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hicup_digester owner: bgruening revisions: - - a2f3a4129052 + - e79c38f1752c tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hicup_deduplicator owner: bgruening revisions: - - 46e5b4782715 + - 2107c2f7a5d7 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: epicseg @@ -5193,31 +5659,55 @@ tools: - name: hicup_mapper owner: bgruening revisions: - - f396b479c2f2 + - be104dee2833 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu -- name: pangolin - owner: iuc +- name: cooler_makebins + owner: lldelisle revisions: - - 03ed9524dcd1 - tool_panel_section_label: Phylogenetics + - c3dc51297bf8 + tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu -- name: hyphy_prime - owner: iuc +- name: cooler_csort_tabix + owner: lldelisle revisions: - - 0407236012e5 - tool_panel_section_label: Phylogenetics + - d56db0e1555d + tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu -- name: hyphy_busted - owner: iuc +- name: cooler_cload_tabix + owner: lldelisle revisions: - - caf23deba39a - tool_panel_section_label: Phylogenetics + - 3ff6eeca667e + tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu -- name: hyphy_bgm - owner: iuc +- name: cooler_balance + owner: lldelisle revisions: - - 4515f2f64e13 + - 8f71aaf6e59d + tool_panel_section_label: Epigenetics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: hicup2juicer + owner: bgruening + revisions: + - b4e7244246e2 + tool_panel_section_label: Epigenetics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: hyphy_prime + owner: iuc + revisions: + - 9d83d1ab0330 + tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: hyphy_busted + owner: iuc + revisions: + - e908c4003bd8 + tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: hyphy_bgm + owner: iuc + revisions: + - 35723f87964d tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard @@ -5229,43 +5719,43 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - a6619171428e + - '841557158611' tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_fubar owner: iuc revisions: - - 6e72195b364a + - 1b893cdead55 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_fade owner: iuc revisions: - - a73fff151e38 + - cf51d3630757 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_sm19 owner: iuc revisions: - - d52a803b2b5c + - a809f93e7e6d tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_meme owner: iuc revisions: - - d5d909979314 + - 5fd8dc04d6af tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_slac owner: iuc revisions: - - 1467fb7e162d + - 2753a5c7597a tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_fel owner: iuc revisions: - - b110a31a9c61 + - ec783806a5c3 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_coffee @@ -5277,7 +5767,7 @@ tools: - name: hyphy_relax owner: iuc revisions: - - 7207313de5a8 + - 5eb9d7217640 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: sarscov2formatter @@ -5310,12 +5800,30 @@ tools: - 4ad8b610ea41 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_related_genomes_nuc + owner: cpt + revisions: + - 5a5fe0a6f78d + tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_related_genomes_prot + owner: cpt + revisions: + - ebcc87a27f9c + tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cpt_xmfa_to_table + owner: cpt + revisions: + - 06d8e28d0bd7 + tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu - name: ete owner: earlhaminst revisions: - - 276e3ee68c37 - - ed74587a13c8 - 2db72467da51 + - ed74587a13c8 + - 276e3ee68c37 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hcluster_sg_parser @@ -5327,8 +5835,8 @@ tools: - name: treebest_best owner: earlhaminst revisions: - - 4f9e5110914b - b78b529f66db + - 4f9e5110914b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: gafa @@ -5355,6 +5863,12 @@ tools: - 41102a84e387 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu +- name: pangolin + owner: iuc + revisions: + - 2f1019071464 + tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: @@ -5364,25 +5878,25 @@ tools: - name: hyphy_conv owner: iuc revisions: - - 6761212b7f1d + - beeeed9665ea tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_annotate owner: iuc revisions: - - 2318841ec191 + - 91cf1290ba6f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_strike_ambigs owner: iuc revisions: - - f5bbd4b34541 + - 31e7f5a25db3 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_cfel owner: iuc revisions: - - 91679ca1480d + - 6960dd62c983 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: usher_matutils @@ -5400,7 +5914,7 @@ tools: - name: hyphy_summary owner: iuc revisions: - - f3e408cc2546 + - 4e7f1a7d18be tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -5409,6 +5923,48 @@ tools: - f78492521996 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu +- name: picrust2_add_descriptions + owner: iuc + revisions: + - 6034c3f3ecf0 + tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: picrust2_hsp + owner: iuc + revisions: + - 6eafc1e01a8c + tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: picrust2_metagenome_pipeline + owner: iuc + revisions: + - 415cb5d91168 + 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: + - 540aedfc81c7 + tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: picrust2_place_seqs + owner: iuc + revisions: + - 680fb3eb574c + tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: picrust2_shuffle_predictions + owner: iuc + revisions: + - 881f2faa5fe7 + tool_panel_section_label: Phylogenetics + tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2pgsnp owner: devteam revisions: @@ -5445,12 +6001,6 @@ tools: - 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tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu -- name: music_manipulate_eset - owner: bgruening - revisions: - - 22232092be53 - tool_panel_section_label: Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu - name: gsc_scran_normalize owner: artbio revisions: - 252eded61848 + tool_panel_section_label: Import/manipulate sc data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cite_seq_count + owner: iuc + revisions: + - 3df3d1b51110 + tool_panel_section_label: Multiomics + tool_shed_url: toolshed.g2.bx.psu.edu +- name: sinto_barcode + owner: iuc + revisions: + - d1b34ac42b8f + tool_panel_section_label: Single-cell + tool_shed_url: toolshed.g2.bx.psu.edu +- name: sinto_fragments + owner: iuc + revisions: + - 29e6bfb2cf49 + tool_panel_section_label: Single-cell + tool_shed_url: toolshed.g2.bx.psu.edu +- name: episcanpy_build_matrix + owner: iuc + revisions: + - 31a21ba2c5ea + tool_panel_section_label: Single-cell + tool_shed_url: toolshed.g2.bx.psu.edu +- name: episcanpy_preprocess + owner: iuc + revisions: + - 29f5f25b9935 + tool_panel_section_label: Single-cell + tool_shed_url: toolshed.g2.bx.psu.edu +- name: episcanpy_cluster_embed + owner: iuc + revisions: + - f4713992f23a + tool_panel_section_label: Single-cell + tool_shed_url: toolshed.g2.bx.psu.edu +- name: velocyto_cli + owner: iuc + revisions: + - 883c33ef3372 + tool_panel_section_label: Single-cell + tool_shed_url: toolshed.g2.bx.psu.edu +- name: baredsc_1d + owner: iuc + revisions: + - 02b1fe7aed76 + tool_panel_section_label: Single-cell + tool_shed_url: toolshed.g2.bx.psu.edu +- name: baredsc_2d + owner: iuc + revisions: + - c29e7bb492bf + tool_panel_section_label: Single-cell + tool_shed_url: toolshed.g2.bx.psu.edu +- name: baredsc_combine_1d + owner: iuc + revisions: + - c32347702e12 + tool_panel_section_label: Single-cell + tool_shed_url: toolshed.g2.bx.psu.edu +- name: baredsc_combine_2d + owner: iuc + revisions: + - 239193b96d72 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: basic_illumination @@ -5700,124 +6310,125 @@ tools: - name: picard owner: devteam revisions: - - 881d7645d1bf - ab1f60c26526 - 1aac2a13842a + - 881d7645d1bf - b502c227b5e6 + - f9242e01365a tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_compare owner: bgruening revisions: - - c89b665b45e4 + - c929a006727f tool_panel_section_label: deepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 4df95152a39e + - 0e49b109abc2 tool_panel_section_label: deepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 3f9dc453c0e8 + - c06951d10364 tool_panel_section_label: deepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 7989c6ddf634 + - 07418a30ed01 tool_panel_section_label: deepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: 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tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu -- name: taxonomy_krona_chart - owner: crs4 - revisions: - - e9005d1f3cfd - tool_panel_section_label: NCBI Blast - tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: @@ -5960,6 +6571,12 @@ tools: - 1e3323a44643 tool_panel_section_label: NCBI Blast tool_shed_url: toolshed.g2.bx.psu.edu +- name: taxonomy_krona_chart + owner: crs4 + revisions: + - c9f8fef1df74 + tool_panel_section_label: NCBI Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate owner: devteam revisions: @@ -5987,7 +6604,7 @@ tools: - name: blastxml_to_top_descr owner: peterjc revisions: - - fe1ed74793c9 + - 8dc4ba7eba5d tool_panel_section_label: NCBI Blast tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_callvariants @@ -6014,40 +6631,10 @@ tools: - 34ac212ef95e tool_panel_section_label: NCBI Blast tool_shed_url: toolshed.g2.bx.psu.edu -- name: hicexplorer_hictransform - owner: bgruening - 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toolshed.g2.bx.psu.edu +- name: hicexplorer_hichyperoptdetectloops + owner: bgruening + revisions: + - 89fb1aab755b + tool_panel_section_label: HiCExplorer + tool_shed_url: toolshed.g2.bx.psu.edu +- name: hicexplorer_hicdifferentialtad + owner: bgruening + revisions: + - 608538d083a2 + tool_panel_section_label: HiCExplorer + tool_shed_url: toolshed.g2.bx.psu.edu +- name: hicexplorer_hicmergedomains + owner: bgruening + revisions: + - 6f725a516914 + tool_panel_section_label: HiCExplorer + tool_shed_url: toolshed.g2.bx.psu.edu - name: bayescan owner: iuc revisions: @@ -6341,13 +6958,13 @@ tools: - name: stacks_assembleperead owner: iuc revisions: - - 6eaf0f9836c8 + - 38ecfb8d52c6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_cstacks owner: iuc revisions: - - be3df81c0353 + - 40cde06ae34a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -6425,67 +7042,67 @@ tools: - name: stacks_populations 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@@ -7042,7 +7533,7 @@ tools: - name: kraken2tax owner: devteam revisions: - - d844fdcce44e + - 50bd98b3ae5a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: scoary @@ -7060,97 +7551,97 @@ tools: - name: humann owner: iuc revisions: - - 6b7622dda516 + - fc6c328c292f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_associate owner: iuc revisions: - - 67b835aace09 + - 1dbfcd56a5d3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_barplot owner: iuc revisions: - - 3f16956afb8a + - 523ae8314ef5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_join_tables owner: iuc revisions: - - cb7de6e163ca + - 6bf703133209 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_reduce_table owner: iuc revisions: - - 324c12894d59 + - 6552df6efe6b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_regroup_table owner: iuc revisions: - - c409a495841f + - e88b731dad59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 71ea608ddfa3 + - 094ad9c068af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - 4137b492233e + - a293a742194f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm owner: iuc revisions: - - 1e55949cf16e + - dcc4123cd3e1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: - - e2c71b852aba + - 97f7bb0851e7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - f00f2c835ac2 + - e9d12c223a80 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler owner: iuc revisions: - - 9540860a506f + - 3f6b689894ac tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - - 4033827c76b8 + - 2d35528d2141 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - 6dee4abadccb + - 1a6cdf55390f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: extract_metaphlan_database owner: iuc revisions: - - b4c750fe0fe3 + - 6efa06ffbac8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: customize_metaphlan_database owner: iuc revisions: - - 892a0629e2ed + - f93a61ef06cf tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: lotus2 @@ -7174,19 +7665,19 @@ tools: - name: coverm_contig owner: iuc revisions: - - 6941d0d453ba + - 1dcea261abbe tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: coverm_genome owner: iuc revisions: - - 134e4e78e754 + - 0ff4b0e5a3bc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: bracken owner: iuc revisions: - - 79450f7fd718 + - 978ae4147c29 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: maaslin2 @@ -7258,31 +7749,31 @@ tools: - name: concoct owner: iuc revisions: - - 147577841bb8 + - 16672a3c9b65 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: concoct_coverage_table owner: iuc revisions: - - 5ded3318cf8a + - 0442e7102125 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: concoct_cut_up_fasta owner: iuc revisions: - - 989f1256d7a9 + - f80e693468d8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: concoct_extract_fasta_bins owner: iuc revisions: - - 505111e8aca5 + - c821c34ab9d9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: concoct_merge_cut_up_clustering owner: iuc revisions: - - 794d4e27925b + - 713189575b8b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: megan_daa2info @@ -7318,7 +7809,7 @@ tools: - name: das_tool owner: iuc revisions: - - bdc1f3694a23 + - e23e7bf8491b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_to_contig2bin @@ -7330,7 +7821,7 @@ tools: - name: recentrifuge owner: iuc revisions: - - 824497684a1f + - b5407cc2bf51 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: aldex2 @@ -7426,7 +7917,7 @@ tools: - name: kleborate owner: iuc revisions: - - '383036561810' + - 959920e3e800 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: polypolish @@ -7438,37 +7929,37 @@ tools: - name: semibin_generate_cannot_links owner: iuc revisions: - - 078414a1226b + - 5ae13a156271 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: semibin owner: iuc revisions: - - 7b382efabb98 + - 6b517dc161e4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: semibin_train owner: iuc revisions: - - 08cc1cd58f38 + - 43df7a4c33a2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: semibin_generate_sequence_features owner: iuc revisions: - - 07bf5268724f + - 0ae1a2636de5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: semibin_bin owner: iuc revisions: - - 474701f91bcd + - 4d561bdc2c31 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: semibin_concatenate_fasta owner: iuc 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toolshed.g2.bx.psu.edu +- name: krakentools_kreport2krona + owner: iuc + revisions: + - 2deaada69b14 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: krakentools_beta_diversity + owner: iuc + revisions: + - c254d75b8b67 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: krakentools_alpha_diversity + owner: iuc + revisions: + - bab112ba9d62 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: krakentools_kreport2mpa + owner: iuc + revisions: + - bb96a1e6583d + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: krakentools_combine_kreports + owner: iuc + revisions: + - 073c867c5244 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: krakentools_extract_kraken_reads + owner: iuc + revisions: + - f329328da134 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: combine_metaphlan2_humann2 + owner: bebatut + revisions: + - 01ac9954c27f + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: mapseq + owner: iuc + revisions: + - a09139ba9c06 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: qiime_collapse_samples @@ -8689,40 +9228,52 @@ tools: - 83fbdf93d51e tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu -- name: ivar_filtervariants +- name: makeeml + owner: ecology + revisions: + - 9cbac7a9b1a3 + tool_panel_section_label: Data and Metadata Management + tool_shed_url: toolshed.g2.bx.psu.edu +- name: eml2eal + owner: ecology + revisions: + - 5c0290c4225a + tool_panel_section_label: Data and Metadata Management + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ivar_consensus owner: iuc revisions: - - 8f8df367470d + - 17f911830a8c tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu -- name: ivar_trim +- name: ivar_removereads owner: iuc revisions: - - f0cc9cf99407 + - 69797fa273c3 tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu -- name: ivar_variants +- name: ivar_trim owner: iuc revisions: - - ed28dd32141c + - 0893a1dbb807 tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu -- name: ivar_removereads +- name: ivar_getmasked owner: iuc revisions: - - 8c05afb547fa + - 2cf4a1cafc16 tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu -- name: ivar_consensus +- name: ivar_variants owner: iuc revisions: - - 1069f6db0a0e + - 045d6d00f606 tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu -- name: ivar_getmasked +- name: ivar_filtervariants owner: iuc revisions: - - 2cf4a1cafc16 + - 1ef5b6e3e09d tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu - name: read_it_and_keep @@ -8740,73 +9291,73 @@ tools: - name: freyja_variants owner: iuc revisions: - - 08c2d81e7942 + - 1f467ed22412 tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu - name: freyja_demix owner: iuc revisions: - - fc6252e78d5b + - c0a0e79d7196 tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu - name: freyja_boot owner: iuc revisions: - - dda5772507b2 + - a09398bc953a tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu - name: freyja_aggregate_plot owner: iuc revisions: - - 0ceb9fb0f4ce + - 1f89eeba299a tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu - name: cooc_mutbamscan owner: iuc revisions: - - 373c1735d31f + - cd0484c5f9f1 tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu - name: cooc_pubmut owner: iuc revisions: - - d04ea6b052c5 + - 0349d8981030 tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu - name: cooc_tabmut owner: iuc revisions: - - 4be399803856 + - 52bd683c6d3f tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu -- name: maxquant - owner: galaxyp +- name: lineagespot + owner: iuc revisions: - - 837224ad1694 - tool_panel_section_label: Proteomics + - 6ddf5a9ce4a5 + tool_panel_section_label: Virology tool_shed_url: toolshed.g2.bx.psu.edu -- name: mqppep_anova +- name: maxquant owner: galaxyp revisions: - - 2d9f216c1048 + - 8934bc76bb52 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - a5e394b36d87 + - bd1535813cfe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstats owner: galaxyp revisions: - - 28434abe6c5c + - b7034eff0db1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid owner: galaxyp revisions: - - abffdfee3021 + - f4be248c3d47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz @@ -8842,19 +9393,19 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: - - 9d1fbff733cf + - d9c3016f7283 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - 2b1868ab3724 + - bf06d196e23d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_psmfeatureextractor owner: galaxyp revisions: - - 047020d9012f + - 63fea23042c4 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: meta_proteome_analyzer @@ -8890,91 +9441,91 @@ tools: - name: openms_novoradapter owner: galaxyp revisions: - - 031adfb7fce0 + - 34dda034b019 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_luciphoradapter owner: galaxyp revisions: - - cab9b21eabf9 + - bf2bf60c8af2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_assaygeneratormetabo owner: galaxyp revisions: - - 11ac8ae77fb7 + - 83f5e5c1209c tool_panel_section_label: Proteomics tool_shed_url: 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tool_shed_url: toolshed.g2.bx.psu.edu - name: psm_validation @@ -8998,7 +9549,7 @@ tools: - name: openms_openswathfeaturexmltotsv owner: galaxyp revisions: - - 72e4bf868316 + - 844c32358954 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring @@ -9010,7 +9561,7 @@ tools: - name: openms_mapstatistics owner: galaxyp revisions: - - 9cdd5faa34d0 + - 045995dc36bc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_digestormotif @@ -9022,655 +9573,655 @@ tools: - name: openms_featurelinkerlabeled owner: galaxyp revisions: - - c781ee2e5e98 + - d9ebdc2e55fe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - 7f6a1f27553e + - 5c2a97a234d6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_spectrafilterwindowmower owner: galaxyp revisions: - - eaf3482c9c63 + - 2876320b80a4 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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 +15570,51 @@ tools: - 5d9a36073ed6 tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu -- name: qiime2__alignment__mafft_add +- 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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 47df64d..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: @@ -41,7 +47,7 @@ tools: .*/alphafold/.*: scheduling: require: - - gpu + - pulsar_gpu roles: training.*: @@ -58,6 +64,9 @@ destinations: max_accepted_cores: 1 params: tmp_dir: true + scheduling: + require: + - local_env singularity: runner: local_runner max_accepted_cores: 1 @@ -81,8 +90,8 @@ destinations: params: default_file_action: remote_transfer dependency_resolution: remote - jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz-test/files/staging" - persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz-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 @@ -117,8 +126,8 @@ destinations: default_file_action: remote_transfer transport: curl dependency_resolution: remote - jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz-test/files/staging" - persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz-test/files/persistent" + jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz/files/staging" + persistence_directory: 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diff --git a/galaxy.yml b/galaxy.yml index eea2431..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'] @@ -41,13 +41,27 @@ - git: repo: 'https://github.com/usegalaxy-eu/libraries-training-repo' dest: /libraries/ - - name: Create the second storage directory + - name: Create the RBD storage directory file: owner: galaxy group: galaxy - path: /rbd/data2 + 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 @@ -74,4 +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 6d84c26..4e0ec4e 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: dde02a8 # 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_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 @@ -32,7 +33,7 @@ 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 @@ -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-cz-test/files/staging" - persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz-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! @@ -103,8 +104,8 @@ galaxy_job_config: default_file_action: remote_transfer transport: curl dependency_resolution: remote - jobs_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz-test/files/staging" - persistence_directory: "/storage/praha5-elixir/home/galaxyeu/pulsar-cz-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 outputs_to_working_directory: false @@ -114,7 +115,6 @@ galaxy_job_config: env: # The cache directory holds the docker containers that get converted - name: SINGULARITY_CACHEDIR - # value: "/tmp/singularity" value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" - name: APPTAINER_CACHEDIR value: "/storage/praha5-elixir/home/galaxyeu/singularity/cache" @@ -159,6 +159,10 @@ 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" @@ -170,7 +174,9 @@ galaxy_config: - 499542@muni.cz - 325073@mail.muni.cz - demko@cesnet.cz - smtp_server: "https://galaxy-cz.grid.cesnet.cz/:587" + # 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 @@ -270,6 +276,12 @@ 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" + - src: files/galaxy/usegalaxy-cz.png + dest: "{{ galaxy_server_dir }}/static/usegalaxy-cz.png" + - src: files/galaxy/elixir_logo.png + dest: "{{ galaxy_server_dir }}/static/elixir_logo.png" + - src: files/galaxy/e-infra_logo.svg + dest: "{{ galaxy_server_dir }}/static/e-infra_logo.svg" galaxy_config_files: - src: files/galaxy/themes.yml @@ -292,6 +304,8 @@ galaxy_config_templates: 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 }}" + - src: templates/galaxy/config/tool_conf.xml.j2 + dest: "{{ galaxy_config_dir }}/tool_conf.xml" galaxy_extra_dirs: - /mnt/data @@ -403,11 +417,8 @@ 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 @@ -418,7 +429,7 @@ 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..c6f7b66 100644 --- a/group_vars/secret.yml +++ b/group_vars/secret.yml @@ -1,39 +1,46 @@ $ANSIBLE_VAULT;1.1;AES256 -34373839636536373136613934353239313537356130353038323138616661363538366635336362 -3030383330383837353763633034323532346536356630620a646636356565336530623663306232 -37386463633665656239353738613362613438663932396563616165323965303034633762636163 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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/templates/galaxy/config/object_store_conf.xml.j2 b/templates/galaxy/config/object_store_conf.xml.j2 index 65460e1..290d799 100644 --- a/templates/galaxy/config/object_store_conf.xml.j2 +++ b/templates/galaxy/config/object_store_conf.xml.j2 @@ -2,12 +2,12 @@ - - + + - - + + diff --git a/templates/galaxy/config/oidc_backends_config.xml b/templates/galaxy/config/oidc_backends_config.xml index 80c1233..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://galaxy-cz.grid.cesnet.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/galaxy/config/tool_conf.xml.j2 b/templates/galaxy/config/tool_conf.xml.j2 new file mode 100644 index 0000000..a2e1bdc --- /dev/null +++ b/templates/galaxy/config/tool_conf.xml.j2 @@ -0,0 +1,606 @@ + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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