somatic_variants.yaml

---
# 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: ucsc_twobittofa
  owner: iuc
  tool_panel_section_id: convert
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: text_processing
  owner: bgruening
  revisions:
  - 0a8c6b61f0f4
  tool_panel_section_id: textutil
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: column_arrange_by_header
  owner: bgruening
  revisions:
  - 6c6d26ff01ff
  tool_panel_section_id: textutil
  tool_shed_url: https://toolshed.g2.bx.psu.edu
# cut_columns tool gets mentioned as alternative to
# column_arrange_by_header in GTN somatic variants tutorial
- name: cut_columns
  owner: devteam
  revisions:
  - cec635fab700
  tool_panel_section_id: textutil
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: samtools_stats
  owner: devteam
  revisions:
  - 145f6d74ff5e
  tool_panel_section_label: "SAM Tools"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: samtools_rmdup
  owner: devteam
  revisions:
  - 586f9e1cdb2b
  tool_panel_section_label: "SAM Tools"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: samtools_view
  owner: iuc
  revisions:
  - b01db2684fa5
  tool_panel_section_label: "SAM Tools"
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: samtools_calmd
  owner: devteam
  revisions:
  - 06dc50b7b711
  tool_panel_section_label: "SAM Tools"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: freebayes
  owner: devteam
  revisions:
  - ef2c525bd8cd
  tool_panel_section_label: "Variant Calling"
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: varscan_somatic
  owner: iuc
  revisions:
  - a57606054bd7
  tool_panel_section_label: "Variant Calling"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: lofreq_indelqual
  owner: iuc
  revisions:
  - 2ae554b4bcca
  tool_panel_section_label: "Variant Calling"
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: lofreq_alnqual
  owner: iuc
  revisions:
  - 2953c43180c0
  tool_panel_section_label: "Variant Calling"
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: lofreq_filter
  owner: iuc
  revisions:
  - fdba1586551d
  tool_panel_section_label: "Variant Calling"
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: lofreq_call
  owner: iuc
  revisions:
  - dfadc322b065
  tool_panel_section_label: "Variant Calling"
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: qualimap_bamqc
  owner: iuc
  revisions:
  - 4a89c6f84425
  tool_panel_section_label: "Quality Control"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: qualimap_multi_bamqc
  owner: iuc
  revisions:
  - adfe9fda2c5f
  tool_panel_section_label: "Quality Control"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: jbrowse
  owner: iuc
  revisions:
  - 9de82b4963e6
  tool_panel_section_label: "Display Data"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: circos
  owner: iuc
  revisions:
  - 014a21767ac4
  tool_panel_section_label: "Display Data"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: trimmomatic
  owner: pjbriggs
  revisions:
  - dfa082f84068
  tool_panel_section_label: "Quality Control"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: gemini_query
  owner: iuc
  revisions:
  - da74170c55c7
  tool_panel_section_label: "Gemini"
  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_annotate
  owner: iuc
  revisions:
  - f2f3bc622a16
  tool_panel_section_label: "Gemini"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
- name: deeptools_bam_coverage
  owner: bgruening
  revisions:
  - 7a7fd0f5f15d
  tool_panel_section_label: "deepTools"
  tool_shed_url: https://toolshed.g2.bx.psu.edu