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galaxy-tools-playbook's Introduction

A ready-to-use Ansible playbook for the Galaxy Tools role.

Before you can use this playbook, you need to install Ansible (version 2.1.2.0+ is required). Note that for the time being, this playbook does not work with Python 3.x.

$ pip install ansible virtualenv

To use, clone this repo and provide a list of tools to install. A sample file if provided in files/sample_tool_list.yaml. , run the playbook:

$ git clone https://github.com/afgane/galaxy-tools-playbook.git
$ cd galaxy-tools-playbook && ansible-galaxy install -f -r requirements_roles.yml -p roles
# Provide a list of tools in files/sample_tool_list.yaml
# Edit tools.yml if you're not targeting Galaxy on localhost:8080
$ ansible-playbook tools.yml -i "localhost," --extra-vars galaxy_tools_api_key=<Admin user API key>

In addition to the output from running the playbook, the installation script will log it's progress in /tmp/galaxy_tool_install.log.

The default settings will run the playbook for an installation of Galaxy on your local machine. To target a different instance of Galaxy, edit tools.yml and set a URL to the Galaxy instance. You can also set the API key there not to have to provide it on the command line.

Updates

To update the version of the galaxy-tools role, run the following command ansible-galaxy install -f -r requirements_roles.yml -p roles

galaxy-tools-playbook's People

Contributors

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galaxy-tools-playbook's Issues

Ansible reports tools are all installed when they are not

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

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