Galaxy ShedTools¶
Each Galaxy instance is customizable, through the web front-end, with different sets of pre installed tools (e.g. SAMtools, BamTools, Bowtie, MACS, RSEM, etc…), exploiting CONDA as default dependency resolver.
New Tools automatically installed using the official GalaxyProject python library Ephemeris.
Current possible pre-sets:
- galaxy-epigen: Galaxy ready for NGS analysis.
- galaxy-rna-workbench: Galaxy ready for RNA Sequencing analysis (original galaxy flavor here).
- galaxy-testing: Galaxy test recipe.
The corresponding recipe on github is downloaded and processed. It is possible to easily add new flavors, just adding new recipes on github.
Create and test Galaxy flavors¶
For each tool you want to install, you must provide tool name
and owner
and one between tool_panel_section_id
and tool_panel_section_label
.
Keys | Required | Default value | Description |
---|---|---|---|
name |
yes | This is is the name of the tool to install | |
owner |
yes | Owner of the Tool Shed repository from where the tools is being installed | |
tool_panel_section_id |
yes, if tool_panel_section_label
not specified |
ID of the tool panel section where you want the
tool to be installed. The section ID can be found
in Galaxy’s shed_tool_conf.xml config file. Note
that the specified section must exist in this file.
Otherwise, the tool will be installed outside any
section. |
|
tool_panel_section_label |
yes, if tool_panel_section_id
not specified |
Display label of a tool panel section where you want the tool to be installed. If it does not exist, this section will be created on the target Galaxy instance (note that this is different than when using the ID). Multi-word labels need to be placed in quotes. Each label will have a corresponding ID created; the ID will be an all lowercase version of the label, with multiple words joined with underscores (e.g., ‘BED tools’ -> ‘bed_tools’). | |
tool_shed_url |
https://toolshed.g2.bx.psu.edu) |
The URL of the Tool Shed from where the tool should be installed. | |
revisions |
latest | A list of revisions of the tool, all of which will attempt to be installed. | |
install_tool_dependencies |
True | True or False - whether to install tool dependencies or not. | |
install_repository_dependencies |
True | True or False - whether to install repo dependencies or not, using classic toolshed packages |
For instance, this is the galaxy TESTING recipe:
---
api_key: <Admin user API key from galaxy_instance>
galaxy_instance: <Galaxy instance IP>
tools:
- name: fastqc
owner: devteam
tool_panel_section_label: 'Tools'
install_resolver_dependencies: True
install_tool_dependencies: False
- name: 'bowtie_wrappers'
owner: 'devteam'
tool_panel_section_label: 'Tools'
install_resolver_dependencies: True
install_tool_dependencies: False
Conda support¶
Conda is a package manager like apt-get, yum, pip, brew or guix and it is, currently, used as default dependency resolver in Galaxy.
References¶
Galaxy flavors: https://github.com/bgruening/docker-galaxy-stable#Extending-the-Docker-Image
Ephemeris: https://ephemeris.readthedocs.io/en/latest/
Ephemeris documentation: https://github.com/galaxyproject/ephemeris
Conda for Galaxy tools dependencies: https://docs.galaxyproject.org/en/master/admin/conda_faq.html