afgane / galaxy-tools-playbook Goto Github PK
View Code? Open in Web Editor NEWA ready-to-use Ansible playbook for the Galaxy Tools role
Home Page: https://github.com/galaxyproject/ansible-galaxy-tools
License: MIT License
A ready-to-use Ansible playbook for the Galaxy Tools role
Home Page: https://github.com/galaxyproject/ansible-galaxy-tools
License: MIT License
Hi, I hope you can help me with this.
My Ansible simply reports that all of my listed tools are already installed, when they aren't!
This is the output from the playbook run...
PLAY [localhost] ***************************************************************
TASK [galaxy_tools : include] **************************************************
skipping: [localhost]
TASK [galaxy_tools : include] **************************************************
included: /home/AD/galaxy/galaxy-tools-playbook/roles/galaxy_tools/tasks/tools.yml for localhost
TASK [galaxy_tools : Create/invoke script virtualenv] **************************
ok: [localhost] => (item=pyyaml)
ok: [localhost] => (item=bioblend)
TASK [galaxy_tools : Place the tool management script] *************************
changed: [localhost]
TASK [galaxy_tools : include] **************************************************
included: /home/AD/galaxy/galaxy-tools-playbook/roles/galaxy_tools/tasks/install_tool_list.yml for localhost
TASK [galaxy_tools : set_fact] *************************************************
ok: [localhost]
TASK [galaxy_tools : get tool list] ********************************************
ok: [localhost]
TASK [galaxy_tools : Install Tool Shed tools] **********************************
[WARNING]: The loop variable 'item' is already in use. You should set the `loop_var` value in the `loop_control` option for the task to
something else to avoid variable collisions and unexpected behavior.
ok: [localhost] => (item={u'owner': u'peterjc', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'align_back_trans'})
ok: [localhost] => (item={u'owner': u'clustalomega', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'clustalomega'})
ok: [localhost] => (item={u'owner': u'bebatut', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'convert_extract_sequence_file'})
ok: [localhost] => (item={u'owner': u'lparsons', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'cutadapt'})
ok: [localhost] => (item={u'owner': u'devteam', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'fasta_clipping_histogram'})
ok: [localhost] => (item={u'owner': u'simon-gladman', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'fasta_extract'})
ok: [localhost] => (item={u'owner': u'galaxyp', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'fasta_merge_files_and_filter_unique_sequences'})
ok: [localhost] => (item={u'owner': u'devteam', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'fasta_nucleotide_changer'})
ok: [localhost] => (item={u'owner': u'simon-gladman', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'fasta_stats'})
ok: [localhost] => (item={u'owner': u'devteam', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'fastq_quality_boxplot'})
ok: [localhost] => (item={u'owner': u'devteam', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'fastq_to_fasta'})
ok: [localhost] => (item={u'owner': u'devteam', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'fastx_artifacts_filter'})
ok: [localhost] => (item={u'owner': u'lparsons', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'fastx_barcode_splitter_enhanced'})
ok: [localhost] => (item={u'owner': u'galaxyp', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'filter_by_fasta_ids'})
ok: [localhost] => (item={u'owner': u'devteam', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'fastx_nucleotides_distribution'})
ok: [localhost] => (item={u'owner': u'devteam', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'fastx_quality_statistics'})
ok: [localhost] => (item={u'owner': u'devteam', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'fastx_reverse_complement'})
ok: [localhost] => (item={u'owner': u'galaxyp', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'filter_by_fasta_ids'})
ok: [localhost] => (item={u'owner': u'peterjc', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'get_orfs_or_cdss'})
ok: [localhost] => (item={u'owner': u'peterjc', u'tool_panel_section_id': u'Fasta Manipulation', u'name': u'secreted_protein_workflow'})
TASK [galaxy_tools : Remove tool management script] ****************************
changed: [localhost]
TASK [galaxy_tools : include] **************************************************
skipping: [localhost]
TASK [galaxy_tools : include] **************************************************
skipping: [localhost]
PLAY RECAP *********************************************************************
localhost : ok=8 changed=2 unreachable=0 failed=0
Why does it point to another repo which seems to do the same thing @afgane?
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