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Update Data Managers on test.org #80

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merged 4 commits into from
Nov 6, 2019
Merged

Update Data Managers on test.org #80

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eba2778
Update Data Managers on test.org
natefoo Oct 30, 2019
942ff03
Only install the manager for rnastar < 2.7.
natefoo Nov 5, 2019
e673e91
Diff shed_data_manager_conf.xml
natefoo Nov 5, 2019
ec7661a
Remove dups from non-lock and temporarily comment the rnastar DM
natefoo Nov 5, 2019
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2 changes: 2 additions & 0 deletions .ci/jenkins.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -530,6 +530,8 @@ function check_for_repo_changes() {
exec_on diff -u "${OVERLAYFS_LOWER}${stc##*${REPO}}" "$stc" || true
log_debug "diff of shed_tool_data_table_conf.xml"
exec_on diff -u "${OVERLAYFS_LOWER}${SHED_TOOL_DATA_TABLE_CONFIG##*${REPO}}" "$SHED_TOOL_DATA_TABLE_CONFIG" || true
log_debug "diff of shed_data_manager.xml"
exec_on diff -u "${OVERLAYFS_LOWER}${SHED_DATA_MANAGER_CONFIG##*${REPO}}" "$SHED_DATA_MANAGER_CONFIG" || true
exec_on "[ -d '${OVERLAYFS_UPPER}${CONDA_PATH##*${REPO}}' -o -d '${OVERLAYFS_UPPER}${SHED_TOOL_DIR##*${REPO}}' ]" || {
log_error "Tool installation failed";
show_logs
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40 changes: 40 additions & 0 deletions test.galaxyproject.org/data_managers.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,40 @@
tool_panel_section_label: Data Managers
tools:
- name: data_manager_hisat_index_builder
owner: devteam
- name: data_manager_twobit_builder
owner: devteam
- name: data_manager_fetch_genome_dbkeys_all_fasta
owner: devteam
- name: data_manager_bwa_mem_index_builder
owner: devteam
- name: data_manager_picard_index_builder
owner: devteam
- name: data_manager_diamond_database_builder
owner: bgruening
- name: data_manager_hisat2_index_builder
owner: iuc
- name: data_manager_bowtie2_index_builder
owner: devteam
- name: data_manager_fetch_genome_all_fasta
owner: devteam
- name: data_manager_snpeff
owner: iuc
- name: data_manager_kallisto_index_builder
owner: iuc
- name: data_manager_manual
owner: iuc
- name: data_manager_plant_tribes_scaffolds_downloader
owner: iuc
- name: data_manager_bowtie_index_builder
owner: iuc
- name: data_manager_fetch_ncbi_taxonomy
owner: devteam
- name: data_manager_gatk_picard_index_builder
owner: devteam
- name: data_manager_sam_fasta_index_builder
owner: devteam
#- name: data_manager_star_index_builder
# owner: iuc
- name: data_manager_gemini_database_downloader
owner: iuc
114 changes: 114 additions & 0 deletions test.galaxyproject.org/data_managers.yml.lock
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@@ -0,0 +1,114 @@
install_repository_dependencies: true
install_resolver_dependencies: true
install_tool_dependencies: false
tool_panel_section_label: Data Managers
tools:
- name: data_manager_hisat_index_builder
owner: devteam
revisions:
- ba11fef120cd
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_twobit_builder
owner: devteam
revisions:
- 9946bc39c834
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_fetch_genome_dbkeys_all_fasta
owner: devteam
revisions:
- 14eb0fc65c62
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_bwa_mem_index_builder
owner: devteam
revisions:
- 46066df8813d
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_picard_index_builder
owner: devteam
revisions:
- b99040168706
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_diamond_database_builder
owner: bgruening
revisions:
- ce62d0912b10
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_hisat2_index_builder
owner: iuc
revisions:
- d210e1f185bd
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_bowtie2_index_builder
owner: devteam
revisions:
- d1d5feb31804
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_fetch_genome_all_fasta
owner: devteam
revisions:
- fb744a070bee
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_snpeff
owner: iuc
revisions:
- 71821eb11274
- d107d20dc6bd
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_kallisto_index_builder
owner: iuc
revisions:
- 6843a0db2da0
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_manual
owner: iuc
revisions:
- 744f607fac50
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_plant_tribes_scaffolds_downloader
owner: iuc
revisions:
- 5833ef61c1f8
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_bowtie_index_builder
owner: iuc
revisions:
- 86e9af693a33
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_fetch_ncbi_taxonomy
owner: devteam
revisions:
- 926847693e4d
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_gatk_picard_index_builder
owner: devteam
revisions:
- b31f1fcb203c
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_sam_fasta_index_builder
owner: devteam
revisions:
- 1865e693d8b2
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers
- name: data_manager_gemini_database_downloader
owner: iuc
revisions:
- f57426daa04d
tool_panel_section_id: data_managers
tool_panel_section_label: Data Managers