docker-galaxy-exome-seq/genetic_disease.yaml at master · bgruening/docker-galaxy-exome-seq · GitHub

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---
# This is a sample file to be used as a reference for populating a list of
# tools that you wish to install into Galaxy from a Tool Shed via the
# `install_tool_shed_tools.py` script.
#
# For each tool you want to install, you must provide the following keys:
#  * name: this is is the name of the tool to install
#  * owner: owner of the Tool Shed repository from where the tools is being
#           installed
# Further, you need to provide **one** of the following two keys:
#  * tool_panel_section_id: 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: 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').
#
# Tou can also specify the following optional keys to further define the
# installation properties:
#  * tool_shed_url: the URL of the Tool Shed from where the tool should be
#                   installed. (default: https://toolshed.g2.bx.psu.edu)
#  * revisions: a list of revisions of the tool, all of which will attempt to
#               be installed. (default: latest)
#  * install_tool_dependencies: True or False - whether to install tool
#                               dependencies or not. (default: True)
#  * install_repository_dependencies: True or False - whether to install repo
#                               dependencies or not. (default: True)


api_key: admin
galaxy_instance: http://localhost:8080
install_resolver_dependencies: True
install_tool_dependencies: False

tools:
- name: freebayes
  owner: devteam
  revisions:
  - 156b60c1530f
  tool_panel_section_label: "Variant Calling"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: bcftools_norm
  owner: iuc
  revisions:
  - 76655fe2c70e
  tool_panel_section_label: "BCF Tools"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: snpeff
  owner: iuc
  revisions:
  - 74aebe30fb52
  tool_panel_section_label: "Variant Annotation"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: multiqc
  owner: iuc
  revisions:
  - bf675f34b056
  tool_panel_section_label: "Display Data"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: samtools_rmdup
  owner: devteam
  revisions:
  - 9129584416e2
  tool_panel_section_label: "SAM Tools"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
# samtool_filter2 is still used in the GTN exome-seq tutorial
# can be removed once tutorial is switched over to samtools_view
- name: samtool_filter2
  owner: devteam
  revisions:
  - 649a225999a5
  tool_panel_section_label: "SAM Tools"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: gemini_load
  owner: iuc
  revisions:
  - 45296e47d565
  tool_panel_section_label: "Gemini"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: gemini_inheritance
  owner: iuc
  revisions:
  - 3123ce7acd0e
  tool_panel_section_label: "Gemini"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: bwa
  owner: devteam
  revisions:
  - 3fe632431b68
  tool_panel_section_label: "Mapping"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: fastqc
  owner: devteam
  revisions:
  - e7b2202befea
  tool_panel_section_label: "Quality Control"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: bamtools_filter
  owner: devteam
  revisions:
  - bd735cae4ce6
  tool_panel_section_label: "SAM Tools"
  tool_shed_url: https://toolshed.g2.bx.psu.edu