diff --git a/README.md b/README.md index 1f2da4e..b019ec1 100644 --- a/README.md +++ b/README.md @@ -73,49 +73,22 @@ The api key can be found in the User -> Preferences -> Manage API Key in Galaxy Later we should use this [role](https://github.com/galaxyproject/ansible-galaxy-tools) to automate this, but there are too many tools to be installed and it is very inpractical for testing purposes. -## Debian 11 - -### TUS +## Notes On ubuntu < 22.04 and Debian < 12 the GLIBC version is incompatible with the ```galaxyproject.tusd``` GLIBC, therfore playbook ends in error. - in `roles/galaxyproject.tusd/defaults/main.yml` you have to set the `tusd_version:` to 'v1.8.0' (tested, possibly higher) -### Ansible +# Debian 11 On Debian 11 the default version of `ansible` is 2.10.08 which fails to extract binaries for TUSd. -- workaround: - - because of Puppet, we need to create dedicated sources.list file for ansible - - `sudo vim /etc/apt/sources.list.d/ansible_ubuntu_focal_main.list` add this line : `deb http://ppa.launchpad.net/ansible/ansible/ubuntu focal main` +- workaround: + - `sudo vim /etc/apt/sources.list` add this line : `deb http://ppa.launchpad.net/ansible/ansible/ubuntu focal main` - then `sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 93C4A3FD7BB9C367` - followed by `sudo apt-get update` and `sudo apt-get install ansible -y` - Note that you might need to `sudo apt remove ansible` `sudo apt autoremove` before you try to install ansible. -### Nginx Upload Module - -Our playbook makes use of `nginx-upload-module`, which is not included by default in any nginx-* distribution from `apt`. -This is a simple recipe for installing nginx with the upload-module. - -``` -sudo apt remove *nginx* -y && -sudo apt autoremove -y && - -wget http://nginx.org/download/nginx-1.24.0.tar.gz && -tar -xzf nginx-1.24.0.tar.gz && -cd nginx-1.24.0/ && -git clone https://github.com/hongzhidao/nginx-upload-module.git && -sudo apt-get install -y libpcre3 libpcre3-dev libssl-dev zlib1g-dev && -./configure --user=nginx --group=nginx --prefix=/etc/nginx --conf-path=/etc/nginx/nginx.conf --sbin-path=/usr/sbin/nginx --http-log-path=/var/log/nginx/access.log --error-log-path=/var/log/nginx/error.log --lock-path=/var/lock/nginx.lock --pid-path=/run/nginx.pid --modules-path=/usr/lib/nginx/modules --http-client-body-temp-path=/var/lib/nginx/body --http-fastcgi-temp-path=/var/lib/nginx/fastcgi --http-proxy-temp-path=/var/lib/nginx/proxy --http-scgi-temp-path=/var/lib/nginx/scgi --http-uwsgi-temp-path=/var/lib/nginx/uwsgi --with-compat --with-debug --with-pcre-jit --with-http_ssl_module --with-http_stub_status_module --with-http_realip_module --with-http_auth_request_module --with-http_v2_module --with-http_dav_module --with-http_slice_module --with-threads --with-http_addition_module --with-http_gunzip_module --with-http_gzip_static_module --with-http_sub_module --add-module=nginx-upload-module && -make && make install -``` - -Note that you might need to `sudo systemctl unmask nginx.service` and remove the `galaxy` and `redirect-ssl` from `/etc/nginx/sites-available and `/etc/nginx/sites-enabled` before running the playbook again. - -### Other issues - - Use `sudo apt install python3-docker` before running the `usegalaxy.rabbitmqserver` role. For influxdb apt key error: https://www.influxdata.com/blog/linux-package-signing-key-rotation/ For proftpd add "LoadModule mod_tls.c" to roles/galaxyproject.proftpd/templates/tls.conf.j2 just before the TLSEngine - 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 16d6328..236ed07 100644 --- a/eu_tool_list.yaml +++ b/eu_tool_list.yaml @@ -5,10 +5,16 @@ tools: - 7ed6dda64a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu +- name: dbbuilder + owner: galaxyp + revisions: + - 983bf725dfc2 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 6ea73833cf67 + - 734abc7ac21d - f5ea3ce9b9b0 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -24,6 +30,12 @@ tools: - a371252a2cf6 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu +- name: spocc_occ + owner: ecology + revisions: + - f64b3c1a80a6 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: @@ -147,19 +159,13 @@ tools: - name: ega_download_client owner: iuc revisions: - - f9db47f68e5e - tool_panel_section_label: Get Data - tool_shed_url: toolshed.g2.bx.psu.edu -- name: dbbuilder - owner: galaxyp - revisions: - - 983bf725dfc2 + - 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 @@ -168,12 +174,6 @@ tools: - b91e1e70f3a1 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu -- name: spocc_occ - owner: ecology - revisions: - - f64b3c1a80a6 - tool_panel_section_label: Get Data - tool_shed_url: toolshed.g2.bx.psu.edu - name: ena_upload owner: iuc revisions: @@ -222,42 +222,6 @@ tools: - 3ddd99c7efee tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu -- name: gff3_rebase - owner: iuc - revisions: - - f7ad5e69aa60 - tool_panel_section_label: Text Manipulation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: basecoverage - owner: devteam - revisions: - - 9c5ff4695c97 - tool_panel_section_label: Operate on Genomic Intervals - tool_shed_url: toolshed.g2.bx.psu.edu -- name: subtract - owner: devteam - revisions: - - 7a2a604ae9c8 - tool_panel_section_label: Join, Subtract and Group - tool_shed_url: toolshed.g2.bx.psu.edu -- name: coverage - owner: devteam - revisions: - - bc9c66c1e9c9 - tool_panel_section_label: Text Manipulation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: cluster - owner: devteam - revisions: - - a126ec6ea0e4 - tool_panel_section_label: Operate on Genomic Intervals - tool_shed_url: toolshed.g2.bx.psu.edu -- name: imagecoordinates_flipaxis - owner: imgteam - revisions: - - f8f1100d0701 - tool_panel_section_label: Imaging - tool_shed_url: toolshed.g2.bx.psu.edu - name: dna_filtering owner: devteam revisions: @@ -270,42 +234,6 @@ tools: - 6595517c2dd8 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu -- name: merge - owner: devteam - revisions: - - 0926c81f382c - tool_panel_section_label: Text Manipulation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: intersect - owner: devteam - revisions: - - 8ddabc73af92 - tool_panel_section_label: Text Manipulation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: flanking_features - owner: devteam - revisions: - - 8307665c4b6c - tool_panel_section_label: Text Manipulation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: get_flanks - owner: devteam - revisions: - - 4cd116158aef - tool_panel_section_label: Text Manipulation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: complement - owner: devteam - revisions: - - e0a23ab32d7f - tool_panel_section_label: Operate on Genomic Intervals - tool_shed_url: toolshed.g2.bx.psu.edu -- name: subtract_query - owner: devteam - revisions: - - 960d5d114184 - tool_panel_section_label: Text Manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: diff owner: bgruening revisions: @@ -336,6 +264,12 @@ tools: - dd40b1e9eebe tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu +- name: imagecoordinates_flipaxis + owner: imgteam + revisions: + - f8f1100d0701 + tool_panel_section_label: Imaging + tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: @@ -357,14 +291,14 @@ tools: - name: text_processing owner: bgruening revisions: - - d698c222f354 - f46f0e4f75c4 + - d698c222f354 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -382,13 +316,7 @@ tools: - name: filter_tabular owner: iuc revisions: - - 4d5aae46f850 - tool_panel_section_label: Text Manipulation - tool_shed_url: toolshed.g2.bx.psu.edu -- name: prinseq - owner: iuc - revisions: - - 1ee282794de3 + - 557ec8d7087d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: jq @@ -409,6 +337,36 @@ tools: - 317ed0ee8bf2 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu +- name: basecoverage + owner: devteam + revisions: + - 9c5ff4695c97 + tool_panel_section_label: Operate on Genomic Intervals + tool_shed_url: toolshed.g2.bx.psu.edu +- name: subtract + owner: devteam + revisions: + - 7a2a604ae9c8 + tool_panel_section_label: Join, Subtract and Group + tool_shed_url: toolshed.g2.bx.psu.edu +- name: prinseq + owner: iuc + revisions: + - 1ee282794de3 + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: cluster + owner: devteam + revisions: + - a126ec6ea0e4 + tool_panel_section_label: Operate on Genomic Intervals + tool_shed_url: toolshed.g2.bx.psu.edu +- name: gff3_rebase + owner: iuc + revisions: + - f7ad5e69aa60 + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header owner: iuc revisions: @@ -421,6 +379,12 @@ tools: - 6ae9724caf4d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu +- name: coverage + owner: devteam + revisions: + - bc9c66c1e9c9 + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_replace owner: kellrott revisions: @@ -433,6 +397,42 @@ tools: - 2e9f3b6ebfbc tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu +- name: merge + owner: devteam + revisions: + - 0926c81f382c + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: intersect + owner: devteam + revisions: + - 8ddabc73af92 + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: flanking_features + owner: devteam + revisions: + - 8307665c4b6c + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: get_flanks + owner: devteam + revisions: + - 4cd116158aef + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: complement + owner: devteam + revisions: + - e0a23ab32d7f + tool_panel_section_label: Operate on Genomic Intervals + tool_shed_url: toolshed.g2.bx.psu.edu +- name: subtract_query + owner: devteam + revisions: + - 960d5d114184 + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu - name: unique owner: bgruening revisions: @@ -442,7 +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 @@ -461,7 +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 @@ -475,18 +475,6 @@ tools: - 6d8444408ff1 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: sample_seqs - owner: peterjc - revisions: - - 7c40a1fbc82e - tool_panel_section_label: Filter and Sort - tool_shed_url: toolshed.g2.bx.psu.edu -- name: seq_filter_by_id - owner: peterjc - revisions: - - 141612f8c3e3 - tool_panel_section_label: Filter and Sort - tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_by_fasta_ids owner: galaxyp revisions: @@ -505,10 +493,16 @@ tools: - b1dbdbf2be18 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu -- name: gffcompare - owner: iuc +- name: sample_seqs + owner: peterjc revisions: - - 0f710191a66d + - 7c40a1fbc82e + tool_panel_section_label: Filter and Sort + tool_shed_url: toolshed.g2.bx.psu.edu +- name: seq_filter_by_id + owner: peterjc + revisions: + - 141612f8c3e3 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: find_in_reference @@ -517,6 +511,12 @@ 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: @@ -532,111 +532,87 @@ tools: - name: datamash_ops owner: iuc revisions: - - 2f3c6f2dcf39 - 4c07ddedc198 + - 2f3c6f2dcf39 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu -- name: crossmap_wig - owner: iuc +- name: cpt_gff_split + owner: cpt revisions: - - e72c320c17c1 + - 8bd03ba8510a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: crossmap_vcf - owner: iuc +- name: cpt_gbk_to_5col + owner: cpt revisions: - - 18f7e96459d2 + - 1bdd481d5c25 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: crossmap_gff - owner: iuc +- name: tabular_to_fasta + owner: devteam revisions: - - 42b239a32349 + - 0b4e36026794 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: crossmap_bed - owner: iuc +- name: fasta_to_tabular + owner: devteam revisions: - - ee86b27291b5 + - 7e801ab2b70e tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: crossmap_bam - owner: iuc +- name: tabular_to_fastq + owner: devteam revisions: - - 158b5b2a164a + - 92034dcbb40a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: msconvert - owner: galaxyp +- name: gfa_to_fa + owner: iuc revisions: - - dd4ba10d0c45 - - 6153e8ada1ee + - e33c82b63727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: bed_to_protein_map +- name: thermo_raw_file_converter owner: galaxyp revisions: - - a7c58b43cbaa + - 19e45916daf9 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: gffcompare_to_bed +- name: msconvert owner: galaxyp revisions: - - ba5368c19dbd + - dd4ba10d0c45 + - 6153e8ada1ee tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: idconvert - owner: galaxyp - revisions: - - 4f7d6bec667f - tool_panel_section_label: Convert Formats - tool_shed_url: toolshed.g2.bx.psu.edu -- name: crossmap_region +- name: interval2maf owner: iuc revisions: - - eb66d7a04bf8 - tool_panel_section_label: Convert Formats - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bigwig_to_bedgraph - owner: bgruening - revisions: - - 3799012ce2ff - tool_panel_section_label: Convert Formats - tool_shed_url: toolshed.g2.bx.psu.edu -- name: tabular_to_fasta - owner: devteam - revisions: - - 0b4e36026794 - tool_panel_section_label: Convert Formats - tool_shed_url: toolshed.g2.bx.psu.edu -- name: fasta_to_tabular - owner: devteam - revisions: - - 7e801ab2b70e + - 7adddc6015c1 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: tabular_to_fastq - owner: devteam +- name: crossmap_wig + owner: iuc revisions: - - 92034dcbb40a + - e72c320c17c1 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: gfa_to_fa +- name: crossmap_vcf owner: iuc revisions: - - e33c82b63727 + - 18f7e96459d2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: thermo_raw_file_converter - owner: galaxyp +- name: crossmap_gff + owner: iuc revisions: - - 19e45916daf9 + - 42b239a32349 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: interval2maf +- name: crossmap_bed owner: iuc revisions: - - 7adddc6015c1 + - ee86b27291b5 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: genebed_maf_to_fasta @@ -645,16 +621,10 @@ tools: - e25ee6bac872 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: samtools_bam_to_cram +- name: crossmap_bam owner: iuc revisions: - - 0b663ca9a961 - tool_panel_section_label: Convert Formats - tool_shed_url: toolshed.g2.bx.psu.edu -- name: gffread - owner: devteam - revisions: - - 154d00cbbf2d + - 158b5b2a164a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: mz_to_sqlite @@ -669,10 +639,16 @@ tools: - 51d54a9c9283 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: ucsc_twobittofa - owner: iuc +- name: bed_to_protein_map + owner: galaxyp revisions: - - 8067dfa00ed2 + - a7c58b43cbaa + tool_panel_section_label: Convert Formats + tool_shed_url: toolshed.g2.bx.psu.edu +- name: gffcompare_to_bed + owner: galaxyp + revisions: + - ba5368c19dbd tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: map_peptides_to_bed @@ -684,7 +660,7 @@ tools: - name: biom_convert owner: iuc revisions: - - 72ed72122deb + - e177a8ea0bf1 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: resize_coordinate_window @@ -693,6 +669,12 @@ tools: - 4eb3cc1f8466 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu +- name: gffread + owner: devteam + revisions: + - 154d00cbbf2d + tool_panel_section_label: Convert Formats + tool_shed_url: toolshed.g2.bx.psu.edu - name: msms_extractor owner: galaxyp revisions: @@ -717,30 +699,72 @@ 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: - c24014d80001 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu +- name: idconvert + owner: galaxyp + revisions: + - 4f7d6bec667f + tool_panel_section_label: Convert Formats + tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 owner: iuc revisions: - b026dae67fba tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu +- name: ucsc_twobittofa + owner: iuc + revisions: + - 8067dfa00ed2 + tool_panel_section_label: Convert Formats + tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_scidx owner: iuc revisions: - 408520e1ae1a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu +- name: bigwig_to_bedgraph + owner: bgruening + revisions: + - 3799012ce2ff + tool_panel_section_label: Convert Formats + tool_shed_url: toolshed.g2.bx.psu.edu - name: bioext_bam2msa owner: iuc revisions: - 359e043a285c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu +- name: crossmap_region + owner: iuc + revisions: + - eb66d7a04bf8 + tool_panel_section_label: Convert Formats + tool_shed_url: toolshed.g2.bx.psu.edu +- name: samtools_bam_to_cram + owner: iuc + revisions: + - 0b663ca9a961 + tool_panel_section_label: Convert Formats + tool_shed_url: toolshed.g2.bx.psu.edu - name: ab1_fastq_converter owner: ecology revisions: @@ -759,258 +783,257 @@ tools: - 4a9ac1df3278 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: filtlong - owner: iuc +- name: cpt_convert_mga + owner: cpt revisions: - - 41b2ad601cf0 - tool_panel_section_label: FASTA/FASTQ + - 1bf722ba06e3 + tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: fasta_compute_length - owner: devteam +- name: cpt_fix_aragorn + owner: cpt revisions: - - 7d37cfda8e00 - tool_panel_section_label: FASTA/FASTQ + - 733cb0807083 + tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastqtofasta +- name: short_reads_trim_seq owner: devteam revisions: - - 297962e79f39 + - 25e6fe525306 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastq_trimmer_by_quality +- name: short_reads_figure_score owner: devteam revisions: - - 8050e091e99b + - b52b9c7aabd9 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastx_renamer +- name: fasta_compute_length owner: devteam revisions: - - b29d37ca9e41 + - 7d37cfda8e00 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastx_reverse_complement +- name: fasta_concatenate_by_species owner: devteam revisions: - 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54a954ee64d4 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: seqkit_fx2tab + owner: iuc + revisions: + - b1b12eaebfa9 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: adapter_removal + owner: iuc + revisions: + - 04d05400d3a6 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu +- name: seqkit_locate + owner: iuc + revisions: + - 6510652376b1 + tool_panel_section_label: FASTA/FASTQ + tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_regex_finder owner: mbernt revisions: @@ -1271,11 +1307,11 @@ tools: - c05232655d00 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: qualimap_counts - owner: iuc +- name: cpt_fasta_remove_id + owner: cpt revisions: - - 1672b9bea89b - tool_panel_section_label: RNA Analysis + - 78222649a59a + tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc @@ -1283,40 +1319,46 @@ tools: - 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- 36677f429310 + - adfe9fda2c5f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: samtools_fastx - owner: iuc +- name: bamtools + owner: devteam + revisions: + - ddb22028b552 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: tag_pileup_frequency + owner: iuc + revisions: + - 580e8bcb6413 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: samtools_markdup + owner: iuc + revisions: + - ce32171c6d44 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: samtools_merge + owner: iuc + revisions: + - 36677f429310 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: samtools_fastx + owner: iuc revisions: - b3d99709fe1a tool_panel_section_label: SAM/BAM @@ -1433,16 +1499,16 @@ tools: - 2e957d4c4b95 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: samtools_calmd +- name: bamtools_filter owner: devteam revisions: - - 92ec40abcdcf + - 108db6635177 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: bamhash - owner: bgruening +- name: samtools_calmd + owner: devteam revisions: - - 63f6f42d112b + - 92ec40abcdcf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -1451,10 +1517,10 @@ tools: - 1e5880498f52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: mosdepth - owner: iuc +- name: bamhash + owner: bgruening revisions: - - 69f93450c57d + - 63f6f42d112b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_paired @@ -1481,28 +1547,28 @@ tools: - e30af4e78cd3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: pileup_interval - owner: devteam +- name: varscan + owner: fcaramia revisions: - - 9c1c0b947e46 + - 51969e284317 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: pileup_parser - owner: devteam +- name: bamutil_diff + owner: iuc revisions: - - 85bedbea8a12 + - c28c4c132459 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: sam2interval - owner: devteam +- name: samtools_ampliconclip + owner: iuc revisions: - - 75557c0908a9 + - 5f3ea90dc6ae tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: tag_pileup_frequency - owner: iuc +- name: revertr2orientationinbam + owner: lldelisle revisions: - - 580e8bcb6413 + - 21ddefab2e4f tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split @@ -1511,28 +1577,10 @@ tools: - 96c9315b0e29 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu -- name: bamtools_filter - owner: devteam - revisions: - - 108db6635177 - tool_panel_section_label: SAM/BAM - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bamutil_diff - owner: iuc - revisions: - - c28c4c132459 - tool_panel_section_label: SAM/BAM - tool_shed_url: toolshed.g2.bx.psu.edu -- name: samtools_ampliconclip +- name: mosdepth owner: iuc revisions: - - 5f3ea90dc6ae - tool_panel_section_label: SAM/BAM - tool_shed_url: toolshed.g2.bx.psu.edu -- name: revertr2orientationinbam - owner: lldelisle - revisions: - - 21ddefab2e4f + - 69f93450c57d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bedtools @@ -1541,9 +1589,15 @@ tools: - b8348686a0b9 - ce3c7f062223 - 07e8b80f278c + - a1a923cd89e8 - dde39ba9c031 - 589e7e57fd6d - - a1a923cd89e8 + 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 @@ -1714,6 +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: @@ -1741,7 +1867,19 @@ 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 + owner: iuc + revisions: + - c784170f3b5e + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: flair_collapse + owner: iuc + revisions: + - 1fdcbfcca71c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: ngmlr @@ -1759,13 +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 @@ -1780,6 +1918,30 @@ tools: - 0f1c34698076 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu +- name: ont_fast5_api_multi_to_single_fast5 + owner: iuc + revisions: + - f98c015cebd8 + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ont_fast5_api_single_to_multi_fast5 + owner: iuc + revisions: + - 435344af6dc9 + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ont_fast5_api_compress_fast5 + owner: iuc + revisions: + - 82c6009bc120 + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ont_fast5_api_fast5_subset + owner: iuc + revisions: + - 0defe443ea04 + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: @@ -1822,6 +1984,12 @@ tools: - ad011fc670d6 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu +- name: porechop + owner: iuc + revisions: + - 543cbeef3949 + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_times owner: iuc revisions: @@ -1900,52 +2068,10 @@ tools: - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu -- name: flair_correct - owner: iuc - revisions: - - c784170f3b5e - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu -- name: flair_collapse - owner: iuc - revisions: - - 1fdcbfcca71c - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu -- name: ont_fast5_api_multi_to_single_fast5 - owner: iuc - revisions: - - f98c015cebd8 - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu -- name: ont_fast5_api_single_to_multi_fast5 - owner: iuc - revisions: - - 435344af6dc9 - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu -- name: ont_fast5_api_compress_fast5 - owner: iuc - revisions: - - 82c6009bc120 - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu -- name: ont_fast5_api_fast5_subset - owner: iuc - revisions: - - 0defe443ea04 - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu -- name: porechop - owner: iuc - revisions: - - 543cbeef3949 - tool_panel_section_label: Nanopore - tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc owner: iuc revisions: - - 3a2f2e24c37e + - dc1500f42073 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: clair3 @@ -1954,16 +2080,10 @@ tools: - 63e02ef6e153 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu -- name: concat - owner: devteam - revisions: - - 73ca13a7ec5f - tool_panel_section_label: Operate on Genomic Intervals - tool_shed_url: toolshed.g2.bx.psu.edu -- name: join +- name: annotation_profiler owner: devteam revisions: - - 718d04143c31 + - 3b33da018e74 tool_panel_section_label: Operate on Genomic Intervals tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -1978,16 +2098,22 @@ tools: - 038ecf54cbec tool_panel_section_label: Operate on Genomic Intervals tool_shed_url: toolshed.g2.bx.psu.edu -- name: translate_bed_sequences - owner: jjohnson +- name: concat + owner: devteam revisions: - - d328db400280 + - 73ca13a7ec5f tool_panel_section_label: Operate on Genomic Intervals tool_shed_url: toolshed.g2.bx.psu.edu -- name: annotation_profiler +- name: join owner: devteam revisions: - - 3b33da018e74 + - 718d04143c31 + tool_panel_section_label: Operate on Genomic Intervals + tool_shed_url: toolshed.g2.bx.psu.edu +- name: translate_bed_sequences + owner: jjohnson + revisions: + - d328db400280 tool_panel_section_label: Operate on Genomic Intervals tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_bed_on_splice_junctions @@ -1996,6 +2122,12 @@ tools: - 915e5c5e02e6 tool_panel_section_label: Operate on Genomic Intervals tool_shed_url: toolshed.g2.bx.psu.edu +- name: extract_genomic_dna + owner: iuc + revisions: + - 5cc8e93ee98f + tool_panel_section_label: Fetch Sequences / Alignments + tool_shed_url: toolshed.g2.bx.psu.edu - name: length_and_gc_content owner: iuc revisions: @@ -2008,34 +2140,40 @@ tools: - 2dfb2fba4081 tool_panel_section_label: Fetch Sequences / Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: extract_genomic_dna +- name: seqkit_locate owner: iuc revisions: - - 5cc8e93ee98f + - 642d73815dd1 tool_panel_section_label: Fetch Sequences / Alignments tool_shed_url: toolshed.g2.bx.psu.edu -- name: seqkit_locate - owner: iuc +- name: braker3 + owner: genouest revisions: - - 642d73815dd1 - tool_panel_section_label: Fetch Sequences / Alignments + - bd103884a09c + tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: bakta - owner: iuc +- name: cpt_phageqc_annotations + owner: cpt revisions: - - 3f0aa1b3e816 + - c3140b08d703 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: tbprofiler - owner: iuc +- name: cpt_gff_extract_seq + owner: cpt revisions: - - 2c68b0c38785 + - ab40380424c9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: annotatemyids +- 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: - - 3e1f6f6d557e + - 94170eee0ad8 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: optitype @@ -2044,12 +2182,24 @@ tools: - fd974c5df8bc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu +- name: prokka + owner: crs4 + revisions: + - 8a22554cdde2 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - 91887494eb97 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu +- name: tbprofiler + owner: iuc + revisions: + - 2c68b0c38785 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu - name: hmmer_nhmmer owner: iuc revisions: @@ -2092,12 +2242,24 @@ tools: - d753d9169482 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu +- name: kofamscan + owner: iuc + revisions: + - 23494763e39e + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 owner: iuc revisions: - 4a7f4b0cc0a3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu +- name: annotatemyids + owner: iuc + revisions: + - cd2480f35935 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite owner: nml revisions: @@ -2146,6 +2308,12 @@ tools: - 31812e7a1315 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu +- name: bp_genbank2gff3 + owner: iuc + revisions: + - 11c3eb512633 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: @@ -2164,6 +2332,36 @@ tools: - 2c7ac12ad75a tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu +- name: transit_tn5gaps + owner: iuc + revisions: + - 3f5fc4b09496 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: transit_resampling + owner: iuc + revisions: + - 885459e1c83b + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: transit_hmm + owner: iuc + revisions: + - 7db455b6434b + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: transit_gumbel + owner: iuc + revisions: + - 8fc50fe60127 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: tetyper + owner: iuc + revisions: + - edcf603bedfd + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: @@ -2176,22 +2374,22 @@ tools: - 28433faa6e42 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: kobas +- name: fargene owner: iuc revisions: - - 20f1b45dea63 + - 239ce9f24386 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: tbvcfreport +- name: kobas owner: iuc revisions: - - 4934c0ac6197 + - 20f1b45dea63 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: tb_variant_filter +- name: gff_to_prot owner: iuc revisions: - - ee4a90760848 + - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: gprofiler_snpense @@ -2206,10 +2404,10 @@ tools: - 7d18814397a7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: gff_to_prot +- name: gprofiler_gost owner: iuc revisions: - - 07d7991bf205 + - bf39cdd007f5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: gprofiler_orth @@ -2224,52 +2422,64 @@ tools: - 8ee097f1763d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu +- name: abricate + owner: iuc + revisions: + - c2ef298da409 + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu - name: blastxml_to_gapped_gff3 owner: iuc revisions: - 561e827baa5f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: goseq +- name: maker owner: iuc revisions: - - 602de62d995b + - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: snap_training +- name: column_maker + owner: devteam + revisions: + - 9cd341095afd + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: socru owner: iuc revisions: - - 2a598c0aa042 + - ce0c9fe32e04 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: fgsea +- name: goseq owner: iuc revisions: - - 17eb1e0d711f + - 602de62d995b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: maker_map_ids +- name: snap_training owner: iuc revisions: - - e906fa778440 + - 2a598c0aa042 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: homer_scanmotifgenomewide +- name: maker_map_ids owner: iuc revisions: - - f15794662a69 + - e906fa778440 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu -- name: homer_findmotifsgenome +- name: fgsea owner: iuc revisions: - 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name: racon owner: bgruening revisions: - - e100a765370e + - 936f0b5e7fcc + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: minia + owner: iuc + revisions: + - 734cd5f1c1b2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: flye @@ -2928,6 +3282,12 @@ tools: - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu +- name: quast + owner: iuc + revisions: + - 72472698a2df + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu - name: miniasm owner: iuc revisions: @@ -2937,25 +3297,25 @@ tools: - name: abyss owner: iuc revisions: - - 7547fcab5d19 + - a929ce596a34 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: idba_ud +- name: unicycler owner: iuc revisions: - - 1542a2fffe0c + - d10bdad2fd17 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: idba_hybrid +- name: idba_ud owner: iuc revisions: - - 5c5806e23338 + - 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tool_shed_url: toolshed.g2.bx.psu.edu -- name: bellerophon - owner: iuc - revisions: - - 25ca5d73aedf - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: links - owner: iuc - revisions: - - 7acd9ade2dd1 - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: mitohifi - owner: bgruening - revisions: - - 99ddbf037d98 - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: gfastats - owner: bgruening - revisions: - - 5799092ffdff - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: smudgeplot - owner: galaxy-australia - revisions: - - 5a0ddb4dc3a4 - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: getorganelle - owner: iuc - revisions: - - 06bcf65179fb - - 611219887a48 - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: minipolish - owner: bgruening +- name: minipolish + owner: bgruening revisions: - 1f9f2edc8cf4 tool_panel_section_label: Assembly @@ -3256,19 +3556,19 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 9eeb13a92d79 + - 94b8c6013083 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - d7ce0ec78e51 + - 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 @@ -3277,66 +3577,6 @@ tools: - 6ee7eb5821f0 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: spades_rnaviralspades - owner: iuc - revisions: - - d5fb354f745d - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: spades_metaviralspades - owner: iuc - revisions: - - 328aa71f0f3c - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: nextdenovo - owner: bgruening - revisions: - - 733eab97b979 - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: spades_metaplasmidspades - owner: iuc - revisions: - - e5a3b75a271f - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: spades_biosyntheticspades - owner: iuc - revisions: - - 051fd2db8a27 - 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: yahs - owner: iuc - revisions: - - 425e63adcc5d - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: velvet - owner: devteam - revisions: - - 920677cd220f - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: cap3 - owner: artbio - revisions: - - d76a0d8a9eac - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu -- name: hapog - owner: iuc - revisions: - - c61bc8bb5f1e - tool_panel_section_label: Assembly - tool_shed_url: toolshed.g2.bx.psu.edu - name: biscot owner: iuc revisions: @@ -3355,6 +3595,12 @@ tools: - 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: @@ -3367,10 +3613,22 @@ tools: - cf54dafa0403 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu -- name: bwa_mem2 +- name: rnaquast owner: iuc revisions: - - bfaa0d22c2e4 + - f89e3c318453 + tool_panel_section_label: Assembly + tool_shed_url: toolshed.g2.bx.psu.edu +- name: megablast_xml_parser + owner: devteam + revisions: + - fbff957a3655 + tool_panel_section_label: Mapping + tool_shed_url: toolshed.g2.bx.psu.edu +- name: megablast_wrapper + owner: devteam + revisions: + - fb2e0e1dac89 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -3379,22 +3637,40 @@ tools: - ecc974513241 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu +- name: lastz + owner: devteam + revisions: + - 37b497aa133f + tool_panel_section_label: Mapping + tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers owner: devteam revisions: - b46e7d48076a tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu +- name: minimap2 + owner: iuc + revisions: + - be1d967337e4 + tool_panel_section_label: Mapping + tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 owner: iuc revisions: - f4af63aaf57a tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: kma +- name: rna_starsolo owner: iuc revisions: - - 95ab864b281a + - 5ef7ec16b04f + tool_panel_section_label: Mapping + tool_shed_url: toolshed.g2.bx.psu.edu +- name: rgrnastar + owner: iuc + revisions: + - 79de45b5069b tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bismark @@ -3404,71 +3680,77 @@ tools: - ff6ee551b153 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu +- name: kma + owner: iuc + revisions: + - 95ab864b281a + tool_panel_section_label: Mapping + tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion owner: iuc revisions: - 137942fac417 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu +- name: bowtie2 + owner: devteam + revisions: + - 03e9b2fbc005 + tool_panel_section_label: Mapping + tool_shed_url: toolshed.g2.bx.psu.edu - name: segemehl owner: rnateam revisions: - 9c0d4ec99ba9 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: bwa - owner: devteam +- name: graphmap_overlap + owner: bgruening revisions: - - 64f11cf59c6e - - e188dc7a68e6 + - d0a712cf0518 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: tophat2 - owner: devteam +- name: graphmap_align + owner: bgruening revisions: - - 16c4255042be + - 190175f4e143 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: megablast_xml_parser +- name: bwa owner: devteam revisions: - - fbff957a3655 + - e188dc7a68e6 + - 64f11cf59c6e tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: megablast_wrapper +- name: tophat2 owner: devteam revisions: - - fb2e0e1dac89 + - 16c4255042be tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: lastz +- name: bowtie_color_wrappers owner: devteam revisions: - - 37b497aa133f + - a3825c73805c tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: minimap2 +- name: winnowmap owner: iuc revisions: - - be1d967337e4 + - 35ea4a8b1ea6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: rna_starsolo +- name: bioext_bealign owner: iuc revisions: - - 13022c3d3076 + - a07a2d9ddd42 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: rgrnastar +- name: bwa_mem2 owner: iuc revisions: - - 3ea5a2a63fa2 - tool_panel_section_label: Mapping - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bowtie2 - owner: devteam - revisions: - - 03e9b2fbc005 + - bfaa0d22c2e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmap @@ -3477,70 +3759,52 @@ tools: - 517464809c33 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: graphmap_overlap - owner: bgruening - revisions: - - d0a712cf0518 - tool_panel_section_label: Mapping - tool_shed_url: toolshed.g2.bx.psu.edu -- name: graphmap_align - owner: bgruening - revisions: - - 190175f4e143 - tool_panel_section_label: Mapping - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bowtie_color_wrappers - owner: devteam - revisions: - - a3825c73805c - tool_panel_section_label: Mapping - tool_shed_url: toolshed.g2.bx.psu.edu -- name: winnowmap +- name: strelka_germline owner: iuc revisions: - - 35ea4a8b1ea6 - tool_panel_section_label: Mapping + - 19481653a22f + tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bioext_bealign +- name: sansa_annotate owner: iuc revisions: - - a07a2d9ddd42 - tool_panel_section_label: Mapping + - b1ca9fce4749 + tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: smgu_frameshift_deletions_checks +- name: strelka_somatic owner: iuc revisions: - - e8971ca74398 + - edbdbc64b397 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: vardict_java +- name: delly_filter owner: iuc revisions: - - e0734e88a104 + - 74f9f312c713 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: vg_view +- name: delly_merge owner: iuc revisions: - - ee62774bb5bd + - 6c44bbc0eaa5 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: vg_deconstruct +- name: delly_call owner: iuc revisions: - - 76d18b1e970b + - c34eab9d5134 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: vg_convert +- name: delly_lr owner: iuc revisions: - - 7366704232b6 + - 97f649646cc1 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: strelka_germline +- name: bcftools_consensus owner: iuc revisions: - - 19481653a22f + - 147de996e34f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: delly_classify @@ -3549,10 +3813,10 @@ tools: - df4300f300e4 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: strelka_somatic +- name: delly_cnv owner: iuc revisions: - - edbdbc64b397 + - 8ad49c4272ea tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfanno @@ -3573,16 +3837,31 @@ tools: - b4b6b660293a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: lumpy_sv +- name: snpfreqplot owner: iuc revisions: - - 88b35d91a662 + - 3d0adeee3f2b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_consensus +- name: variant_analyzer owner: iuc revisions: - - 147de996e34f + - 3f1dbd2c59bf + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: snpsift + owner: iuc + revisions: + - 09d6806c609e + - 2b3e65a4252f + - b04635ebfab0 + - 5fab4f81391d + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: lumpy_sv + owner: iuc + revisions: + - 88b35d91a662 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lumpy_prep @@ -3609,6 +3888,12 @@ tools: - 16d22eee0fe3 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu +- name: artic_minion + owner: iuc + revisions: + - 468b90c41cde + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu - name: cutesv owner: iuc revisions: @@ -3621,6 +3906,24 @@ tools: - 93c4b04a0769 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu +- name: vardict_java + owner: iuc + revisions: + - e0734e88a104 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: control_freec + owner: iuc + revisions: + - f923c54a17ee + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: gatk4_mutect2 + owner: iuc + revisions: + - 53ce8be43212 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat owner: iuc revisions: @@ -3651,6 +3954,12 @@ tools: - 971e07ca4456 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu +- name: seqwish + owner: iuc + revisions: + - 0c415ba215e7 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu - name: odgi_viz owner: iuc revisions: @@ -3663,6 +3972,24 @@ tools: - 6584dfcc7165 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu +- name: vg_view + owner: iuc + revisions: + - ee62774bb5bd + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vg_deconstruct + owner: iuc + revisions: + - 76d18b1e970b + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vg_convert + owner: iuc + revisions: + - 7366704232b6 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: @@ -3825,22 +4152,40 @@ tools: - f01b2c9506b9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_plugin_frameshifts +- 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: + - 36960e552ddc + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bcftools_cnv + owner: iuc + revisions: + - 6d35a3780bfd + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: snp_dists owner: iuc revisions: - - 399b40b2bcab + - 1959cc43b414 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_plugin_color_chrs +- name: tag_pileup_frequency owner: iuc revisions: - - 36960e552ddc + - 6432735cdb22 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_cnv +- name: snp_sites owner: iuc revisions: - - 6d35a3780bfd + - 5804f786060d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: exomedepth @@ -3855,25 +4200,30 @@ tools: - a5937157062f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu +- name: snpeff + owner: iuc + revisions: + - 5c7b70713fb5 + - 5b80f544c67f + - e8adfc4c0a6b + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_somatic owner: iuc revisions: - cf8ffc79db67 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools +- name: basil owner: iuc revisions: - - bdd0cb7fbedf + - e6ef29001647 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpsift +- name: bcftools owner: iuc revisions: - - 5fab4f81391d - - 09d6806c609e - - 2b3e65a4252f - - b04635ebfab0 + - bdd0cb7fbedf tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: vt_variant_tools @@ -3882,76 +4232,76 @@ tools: - 6e073fc99d9c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: varscan_copynumber - owner: iuc +- name: naive_variant_caller + owner: blankenberg revisions: - - 9f8dbbbc0267 + - aff38ea879f1 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: sansa_annotate +- name: snpsift_genesets owner: iuc revisions: - - b1ca9fce4749 + - d12a810c837e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: varscan_version_2 - owner: devteam +- name: snpsift_dbnsfp + owner: iuc revisions: - - bc1e0cd41241 + - 4e21e4f2bc48 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: varscan_mpileup +- name: snpsift_dbnsfp_generic owner: iuc revisions: - - db94eadb92c1 + - a7cbaf3beadd tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpeff_to_peptides - owner: jjohnson +- name: varscan_copynumber + owner: iuc revisions: - - 80eff5812b2a + - 9f8dbbbc0267 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_plugin_split_vep - owner: iuc +- name: varscan_version_2 + owner: devteam revisions: - - d55feecb6dc1 + - bc1e0cd41241 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: delly_filter +- name: varscan_mpileup owner: iuc revisions: - - 74f9f312c713 + - db94eadb92c1 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: delly_merge - owner: iuc +- name: snpeff_cds_report + owner: jjohnson revisions: - - 6c44bbc0eaa5 + - fbb6510186df tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: delly_call - owner: iuc +- name: snpeff_to_peptides + owner: jjohnson revisions: - - c34eab9d5134 + - 80eff5812b2a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: delly_lr +- name: bcftools_plugin_split_vep owner: iuc revisions: - - 97f649646cc1 + - d55feecb6dc1 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: delly_cnv - owner: iuc +- name: allele_counts + owner: nick revisions: - - 8ad49c4272ea + - 31361191d2d2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpfreqplot +- name: get_hrun owner: iuc revisions: - - 3d0adeee3f2b + - 84f70ce0b830 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -3966,10 +4316,10 @@ tools: - abc3ced31cd1 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: variant_analyzer +- name: bcftools_stats owner: iuc revisions: - - 3f1dbd2c59bf + - a2f8dc22d7c0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -4026,34 +4376,28 @@ tools: - 3f62d4939d54 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: bcftools_stats - owner: iuc - revisions: - - a2f8dc22d7c0 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: control_freec +- name: beagle owner: iuc revisions: - - f923c54a17ee + - f75bf16ac901 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: artic_guppyplex +- name: deepvariant owner: iuc revisions: - - 00e20a06ff1e + - 918c8b94c8d8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: artic_minion +- name: king owner: iuc revisions: - - 468b90c41cde + - 1932808c6fab tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: gatk4_mutect2 +- name: artic_guppyplex owner: iuc revisions: - - 53ce8be43212 + - 00e20a06ff1e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: pharmcat @@ -4068,10 +4412,10 @@ tools: - ee407fae3ccd tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: seqwish +- name: ensembl_vep owner: iuc revisions: - - 0c415ba215e7 + - fdbd97ff825e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: breseq @@ -4080,22 +4424,10 @@ tools: - 0d18a3ba2d1c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snp_dists - owner: iuc - revisions: - - 1959cc43b414 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: tag_pileup_frequency - owner: iuc - revisions: - - 6432735cdb22 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: snp_sites +- name: vcf2maf owner: iuc revisions: - - 5804f786060d + - e8510e04a86a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -4104,252 +4436,286 @@ tools: - 262bba5b90ef tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpeff - owner: iuc - revisions: - - e8adfc4c0a6b - - 5b80f544c67f - - 5c7b70713fb5 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu -- name: basil - owner: iuc - revisions: - - e6ef29001647 - tool_panel_section_label: Variant Calling - tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf owner: iuc revisions: - - 78df8fc2b3ab + - d9965e143053 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cnvkit_access owner: iuc revisions: - - 22878d2aff05 + - 9f18bcf53f92 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cnvkit_antitarget owner: iuc revisions: - - 98086253a782 + - b52fa1df3bc4 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cnvkit_autobin owner: iuc revisions: - - fff49e30af46 + - 94e1d19c8190 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cnvkit_batch owner: iuc revisions: - - e3bbe8171af9 + - 4653aeb60243 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cnvkit_call owner: iuc revisions: - - cc56d01a0b36 + - 0a5e2fc51dfb tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cnvkit_coverage owner: iuc revisions: - - 283ab3112eea + - 5602cbf1153b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cnvkit_diagram owner: iuc revisions: - - 9d18753f47b4 + - 697c61206f5f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cnvkit_fix owner: iuc revisions: - - f64acbe71392 + - dc0fb5f07231 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cnvkit_heatmap owner: iuc revisions: - - ff6b3f5a7ffb + - d8c45afa221c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cnvkit_reference owner: iuc revisions: - - 83470ecad188 + - 0c3db8ec44b0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cnvkit_scatter owner: iuc revisions: - - ec9731970f8b + - 3323a7867128 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cnvkit_segment owner: iuc revisions: - - 9d9a8f230a2f + - c4a22d0fdba5 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cnvkit_target owner: iuc revisions: - - 0350116f0c25 + - 876630eb0680 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: naive_variant_caller - owner: blankenberg +- name: smgu_frameshift_deletions_checks + owner: iuc revisions: - - aff38ea879f1 + - e8971ca74398 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpsift_genesets - owner: iuc +- name: manta + owner: artbio revisions: - - d12a810c837e + - cb5691381acb tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpsift_dbnsfp +- name: beacon2_csv2xlsx owner: iuc revisions: - - 4e21e4f2bc48 + - ba4ed464f8b6 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpsift_dbnsfp_generic +- name: beacon2_pxf2bff owner: iuc revisions: - - a7cbaf3beadd + - 30605b5fc43f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: snpeff_cds_report - owner: jjohnson +- name: beacon2_vcf2bff + owner: iuc revisions: - - fbb6510186df + - 0a757835a745 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: allele_counts - owner: nick +- name: cnvkit_breaks + owner: iuc revisions: - - 31361191d2d2 + - ef9a50eb20ce tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: get_hrun +- name: cnvkit_genemetrics owner: iuc revisions: - - 84f70ce0b830 + - 2b53415d4f3c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: beagle +- name: cnvkit_segmetrics owner: iuc revisions: - - f75bf16ac901 + - d9cb65e1f756 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: deepvariant +- name: cnvkit_sex owner: iuc revisions: - - 918c8b94c8d8 + - 3316bd294f6f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu -- name: king +- name: crispr_studio owner: iuc revisions: - - 1932808c6fab - tool_panel_section_label: Variant Calling + - 7346619ad005 + tool_panel_section_label: Genome editing tool_shed_url: toolshed.g2.bx.psu.edu -- name: ensembl_vep +- name: mageck_test owner: iuc revisions: - 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owner: devteam +- name: ggplot2_heatmap + owner: iuc revisions: - - 6f134426c2b0 + - 10515715c940 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu -- name: gmaj - owner: devteam +- name: ggplot2_violin + owner: iuc revisions: - - 2cd5ee197ec7 + - 0e7290688b50 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu -- name: pe_histogram +- name: ggplot2_point owner: iuc revisions: - - bd1416eea1f0 + - 3b12bf9b4b87 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu -- name: xy_plot - owner: devteam +- name: ggplot2_histogram + owner: iuc revisions: - - 319fa5a9fc1b + - b0d96516e6a5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu -- name: pygenometracks +- name: newick_utils owner: iuc revisions: - - 59fd173ac850 + - b4163d2f64ab tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage @@ -12430,12 +12808,30 @@ tools: - ddddce450736 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu +- name: intervene + owner: iuc + revisions: + - 21beb30956c2 + tool_panel_section_label: Graph/Display Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: taxonomy_krona_chart + owner: crs4 + revisions: + - 73486cc6170e + tool_panel_section_label: Graph/Display Data + tool_shed_url: toolshed.g2.bx.psu.edu - name: pathview owner: iuc revisions: - f1691de443a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu +- name: export2graphlan + owner: iuc + revisions: + - b16989c1e3a7 + tool_panel_section_label: Graph/Display Data + tool_shed_url: toolshed.g2.bx.psu.edu - name: venn_list owner: peterjc revisions: @@ -12448,17 +12844,41 @@ tools: - 83c573f2e73c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_heatmap2 + owner: iuc + revisions: + - 53460afd5115 + tool_panel_section_label: Graph/Display Data + tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - 7b2455348edf tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_pca + owner: iuc + revisions: + - b1268b7544d3 + tool_panel_section_label: Graph/Display Data + tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_color_plot owner: iuc revisions: - - 980917b09eb8 - e4b5401adcec + - 980917b09eb8 + tool_panel_section_label: Graph/Display Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: graphlan + owner: iuc + revisions: + - 8f62f666dcb6 + tool_panel_section_label: Graph/Display Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: graphlan_annotate + owner: iuc + revisions: + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: tsne @@ -12467,12 +12887,30 @@ tools: - 53cfe6f313b3 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu +- name: krona_text + owner: saskia-hiltemann + revisions: + - b14f1444e464 + tool_panel_section_label: Graph/Display Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: mummer + owner: peterjc + revisions: + - d9f3d4779507 + tool_panel_section_label: Graph/Display Data + tool_shed_url: toolshed.g2.bx.psu.edu - name: karyotype_plot owner: guru-ananda revisions: - d810aa84ee6a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu +- name: pe_histogram + owner: iuc + revisions: + - bd1416eea1f0 + tool_panel_section_label: Graph/Display Data + tool_shed_url: toolshed.g2.bx.psu.edu - name: pretext_snapshot owner: iuc revisions: @@ -12485,40 +12923,46 @@ tools: - fec313f5c889 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu +- name: geneiobio + owner: iuc + revisions: + - fc53fcdbe548 + tool_panel_section_label: Graph/Display Data + tool_shed_url: toolshed.g2.bx.psu.edu - name: cif2cell owner: muon-spectroscopy-computational-project revisions: - - 60ad7a4f1faf + - e5f1ac42b063 tool_panel_section_label: Muon Spectroscopy tool_shed_url: toolshed.g2.bx.psu.edu - name: muspinsim_config owner: muon-spectroscopy-computational-project revisions: - - 331d0776abb4 + - e1e338f56656 tool_panel_section_label: Muon Spectroscopy tool_shed_url: toolshed.g2.bx.psu.edu - name: muspinsim owner: muon-spectroscopy-computational-project revisions: - - 136ed45d1ea9 + - e002cee8f707 tool_panel_section_label: Muon Spectroscopy tool_shed_url: toolshed.g2.bx.psu.edu - name: muspinsim_plot owner: muon-spectroscopy-computational-project revisions: - - d7a0a31760b1 + - e15e8800c39e tool_panel_section_label: Muon Spectroscopy tool_shed_url: toolshed.g2.bx.psu.edu - name: pm_asephonons owner: muon-spectroscopy-computational-project revisions: - - dd3ca8457fcd + - fd28cbdb134e tool_panel_section_label: Muon Spectroscopy tool_shed_url: toolshed.g2.bx.psu.edu - name: pm_symmetry owner: muon-spectroscopy-computational-project revisions: - - 620ab6826b9b + - c062cefbb20f tool_panel_section_label: Muon Spectroscopy tool_shed_url: toolshed.g2.bx.psu.edu - name: pm_yaml_config @@ -12536,7 +12980,7 @@ tools: - name: pm_uep_opt owner: muon-spectroscopy-computational-project revisions: - - 523d44fcd03f + - eea73e1f65cb tool_panel_section_label: Muon Spectroscopy tool_shed_url: toolshed.g2.bx.psu.edu - name: pm_dftb_opt @@ -12548,9 +12992,21 @@ tools: - name: pm_muairss_read owner: muon-spectroscopy-computational-project revisions: - - 276a25ab05f2 + - 40071ff77285 + tool_panel_section_label: Muon Spectroscopy + tool_shed_url: toolshed.g2.bx.psu.edu +- name: muspinsim_combine + owner: muon-spectroscopy-computational-project + revisions: + - 06aabd70b869 tool_panel_section_label: Muon Spectroscopy tool_shed_url: toolshed.g2.bx.psu.edu +- name: mutate_snp_codon + owner: devteam + revisions: + - 8f0af7251167 + tool_panel_section_label: Evolution + tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: @@ -12563,22 +13019,16 @@ tools: - f9cb3a4339c2 tool_panel_section_label: Evolution tool_shed_url: toolshed.g2.bx.psu.edu -- name: rapidnj +- name: structure owner: iuc revisions: - - 9f4a66e22580 - tool_panel_section_label: Evolution - tool_shed_url: toolshed.g2.bx.psu.edu -- name: mutate_snp_codon - owner: devteam - revisions: - - 8f0af7251167 + - 4bd5e5dbc6c5 tool_panel_section_label: Evolution tool_shed_url: toolshed.g2.bx.psu.edu -- name: structure +- name: rapidnj owner: iuc revisions: - - 4bd5e5dbc6c5 + - 9f4a66e22580 tool_panel_section_label: Evolution tool_shed_url: toolshed.g2.bx.psu.edu - name: tn93 @@ -12605,6 +13055,12 @@ tools: - 1d2ec0b0a0a7 tool_panel_section_label: Evolution tool_shed_url: toolshed.g2.bx.psu.edu +- name: weblogo3 + owner: devteam + revisions: + - dc25a5169a91 + tool_panel_section_label: Motif Tools + tool_shed_url: toolshed.g2.bx.psu.edu - name: meme_psp_gen owner: iuc revisions: @@ -12635,12 +13091,6 @@ tools: - cc100e0f61f4 tool_panel_section_label: Motif Tools tool_shed_url: toolshed.g2.bx.psu.edu -- name: weblogo3 - owner: devteam - revisions: - - dc25a5169a91 - tool_panel_section_label: Motif Tools - tool_shed_url: toolshed.g2.bx.psu.edu - name: chipeakanno_annopeaks owner: kpbioteam revisions: @@ -12953,12 +13403,6 @@ tools: - 810820a0d45c tool_panel_section_label: Climate Analysis tool_shed_url: toolshed.g2.bx.psu.edu -- name: apollo_delete_features - owner: gga - revisions: - - f8d6315223d8 - tool_panel_section_label: Apollo - tool_shed_url: toolshed.g2.bx.psu.edu - name: apollo_list_organism owner: gga revisions: @@ -12971,22 +13415,22 @@ tools: - 1a2404ca43f9 tool_panel_section_label: Apollo tool_shed_url: toolshed.g2.bx.psu.edu -- name: apollo_delete_organism +- name: apollo_iframe owner: gga revisions: - - 8f4c1d40e893 + - 300a6bebd790 tool_panel_section_label: Apollo tool_shed_url: toolshed.g2.bx.psu.edu -- name: apollo_create_or_update +- name: apollo_fetch_jbrowse owner: gga revisions: - - 3d693b93991f + - d91f4bc313d3 tool_panel_section_label: Apollo tool_shed_url: toolshed.g2.bx.psu.edu -- name: apollo_iframe +- name: apollo_feat_from_gff3 owner: gga revisions: - - 300a6bebd790 + - 250745643de2 tool_panel_section_label: Apollo tool_shed_url: toolshed.g2.bx.psu.edu - name: apollo_export @@ -12995,16 +13439,22 @@ tools: - f6e09a37bc8b tool_panel_section_label: Apollo tool_shed_url: toolshed.g2.bx.psu.edu -- name: apollo_feat_from_gff3 +- name: apollo_create_or_update owner: gga revisions: - - 250745643de2 + - 3d693b93991f tool_panel_section_label: Apollo tool_shed_url: toolshed.g2.bx.psu.edu -- name: apollo_fetch_jbrowse +- name: apollo_delete_organism owner: gga revisions: - - d91f4bc313d3 + - 8f4c1d40e893 + tool_panel_section_label: Apollo + tool_shed_url: toolshed.g2.bx.psu.edu +- name: apollo_delete_features + owner: gga + revisions: + - f8d6315223d8 tool_panel_section_label: Apollo tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler @@ -13157,6 +13607,12 @@ tools: - 3a686b6aa7fc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu +- name: spyboat + owner: iuc + revisions: + - 07a85bc414ba + tool_panel_section_label: Imaging + tool_shed_url: toolshed.g2.bx.psu.edu - name: imagej2_binary_to_edm owner: imgteam revisions: @@ -13217,6 +13673,12 @@ tools: - 39b2bc251b2f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu +- name: idr_download_by_ids + owner: iuc + revisions: + - cbd605a24336 + tool_panel_section_label: Imaging + tool_shed_url: toolshed.g2.bx.psu.edu - name: wsi_extract_top_view owner: imgteam revisions: @@ -13331,6 +13793,12 @@ tools: - 2be338fc671e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu +- name: image_info + owner: imgteam + revisions: + - 7b6d9412c7f8 + tool_panel_section_label: Imaging + tool_shed_url: toolshed.g2.bx.psu.edu - name: detection_viz owner: imgteam revisions: @@ -13355,6 +13823,12 @@ tools: - 70316d792fc9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu +- name: bfconvert + owner: imgteam + revisions: + - 10eed33aa9b2 + tool_panel_section_label: Imaging + tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: @@ -13376,8 +13850,8 @@ tools: - name: points2labelimage owner: imgteam revisions: - - 9bd039f46843 - dcc8c1d6af48 + - 9bd039f46843 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: concat_channels @@ -13494,12 +13968,6 @@ tools: - e0af18405e37 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu -- name: spyboat - owner: iuc - revisions: - - 07a85bc414ba - tool_panel_section_label: Imaging - tool_shed_url: toolshed.g2.bx.psu.edu - name: points_association_nn owner: imgteam revisions: @@ -13512,28 +13980,10 @@ tools: - a9972c993bed tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu -- name: idr_download_by_ids - owner: iuc - revisions: - - cbd605a24336 - tool_panel_section_label: Imaging - tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images owner: imgteam revisions: - - bf590a9733ed - tool_panel_section_label: Imaging - tool_shed_url: toolshed.g2.bx.psu.edu -- name: image_info - owner: imgteam - revisions: - - 7b6d9412c7f8 - tool_panel_section_label: Imaging - tool_shed_url: toolshed.g2.bx.psu.edu -- name: bfconvert - owner: imgteam - revisions: - - f3360fbeda64 + - b74693340624 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler4 @@ -13722,6 +14172,36 @@ tools: - 5b31641e6d30 tool_panel_section_label: Biodiversity data exploration tool_shed_url: toolshed.g2.bx.psu.edu +- name: ecoregion_clara_cluster + owner: ecology + revisions: + - 32849c52aa54 + tool_panel_section_label: Ecoregionalization + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ecoregion_brt_analysis + owner: ecology + revisions: + - f0d6938d0451 + tool_panel_section_label: Ecoregionalization + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ecoregion_eco_map + owner: ecology + revisions: + - 3d750279158b + tool_panel_section_label: Ecoregionalization + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ecoregion_cluster_estimate + owner: ecology + revisions: + - 0f6542d0986e + tool_panel_section_label: Ecoregionalization + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ecoregion_taxa_seeker + owner: ecology + revisions: + - e3cd588fd14a + tool_panel_section_label: Ecoregionalization + tool_shed_url: toolshed.g2.bx.psu.edu - name: astropy_fits2bitmap owner: astroteam revisions: @@ -13740,6 +14220,12 @@ tools: - be9ce7d4ccbf tool_panel_section_label: Astronomy tool_shed_url: toolshed.g2.bx.psu.edu +- name: astronomical_archives + owner: astroteam + revisions: + - 0ddfc343f9f9 + tool_panel_section_label: Astronomy + tool_shed_url: toolshed.g2.bx.psu.edu - name: onto_tk_get_ancestor_terms owner: iuc revisions: @@ -13914,6 +14400,18 @@ tools: - 7ad420b1be89 tool_panel_section_label: HCA-Single Cell tool_shed_url: toolshed.g2.bx.psu.edu +- name: hca_matrix_downloader + owner: ebi-gxa + revisions: + - 2e81fbe036b2 + tool_panel_section_label: HCA-Single Cell + tool_shed_url: toolshed.g2.bx.psu.edu +- name: gtf2gene_list + owner: ebi-gxa + revisions: + - b6354c917ef9 + tool_panel_section_label: Single Cell Utils and Viz + tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_cell_browser owner: ebi-gxa revisions: @@ -13938,18 +14436,6 @@ tools: - 640982866dfe tool_panel_section_label: HCA-Single Cell tool_shed_url: toolshed.g2.bx.psu.edu -- name: hca_matrix_downloader - owner: ebi-gxa - revisions: - - 2e81fbe036b2 - tool_panel_section_label: HCA-Single Cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: gtf2gene_list - owner: ebi-gxa - revisions: - - b6354c917ef9 - tool_panel_section_label: HCA-Single Cell - tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa owner: ebi-gxa revisions: diff --git a/files/galaxy/e-infra_logo.svg b/files/galaxy/e-infra_logo.svg new file mode 100644 index 0000000..0a16032 --- /dev/null +++ b/files/galaxy/e-infra_logo.svg @@ -0,0 +1,290 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/files/galaxy/elixir_logo.png b/files/galaxy/elixir_logo.png new file mode 100644 index 0000000..486cd69 Binary files /dev/null and b/files/galaxy/elixir_logo.png differ diff --git a/files/galaxy/usegalaxy-cz.png b/files/galaxy/usegalaxy-cz.png new file mode 100644 index 0000000..6e3e5aa Binary files /dev/null and b/files/galaxy/usegalaxy-cz.png differ diff --git a/files/galaxy/welcome.html b/files/galaxy/welcome.html index 549c600..49fb52c 100644 --- a/files/galaxy/welcome.html +++ b/files/galaxy/welcome.html @@ -6,24 +6,24 @@
-
-

Welcome to UseGalaxy CZ

-
+

+ UsegalaxyCZ logo +

+

The Czech Galaxy instance

+

Welcome to the public Galaxy instance of E-Infra CZ and ELIXIR CZECH REPUBLIC hosted at MetaCentrum to enable accessible, reproducible and transparent computational research. Galaxy supports thousands of documented and maintained tools that are free to use. +

+
- e-infra + e-infra
- elixir + elixir

-
-
-

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

-

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

diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index b657dbb..4e0ec4e 100644 --- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -276,6 +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 @@ -298,6 +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 diff --git a/group_vars/secret.yml b/group_vars/secret.yml index eb3d58a..c6f7b66 100644 --- a/group_vars/secret.yml +++ b/group_vars/secret.yml @@ -1,46 +1,46 @@ $ANSIBLE_VAULT;1.1;AES256 -30303337656261656337666563646337353937343463663462643364653435633864396434373730 -3861376165613462656536633532326331373265663836350a663963613461383734613038653462 -61646663323835363465333536323961613836306564623431303630326665313462633061336634 -6662346165646435300a373938366139356565626434633637616133313530613061363037343439 -38366234393537653534303038366264663336636336663038303564646163653864316235383263 -36613032646261366163313132316531396439393334653833366533353332363734303438653163 -63323464366335666432396634386231636662643661393233393564666135666634623065623832 -30393261666363323337336532656433383364396134616230346162303637363734323938316238 -33393665336562646138613165303562646463623033343631663065343735616536313638303830 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