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:

  1. galaxy-epigen: Galaxy ready for NGS analysis.
  2. galaxy-rna-workbench: Galaxy ready for RNA Sequencing analysis (original galaxy flavor here).
  3. 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 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>

- 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.