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rna_workbench.yml
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rna_workbench.yml
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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:
# RNA Alignment
- name: compalignp
owner: rnateam
tool_panel_section_label: "RNA Alignment"
- name: mafft
owner: rnateam
tool_panel_section_label: "RNA Alignment"
- name: suite_locarna
owner: rnateam
tool_panel_section_label: "RNA Alignment"
- name: locarna_multiple
owner: rnateam
tool_panel_section_label: "RNA Alignment"
revisions:
- 8414fea2a6fd
- name: segmentation_fold
owner: yhoogstrate
tool_panel_section_label: "RNA Structure Analysis"
- name: selectsequencesfrommsa
owner: rnateam
tool_panel_section_label: "RNA Alignment"
- name: rnalien
owner: rnateam
tool_panel_section_label: "RNA Alignment"
- name: cmv
owner: rnateam
tool_panel_section_label: "RNA Alignment"
# Ribosome Profiling
- name: ribotaper
owner: rnateam
tool_panel_section_label: "Ribosome Profiling"
install_resolver_dependencies: false
# RNA-Seq
- name: sortmerna
owner: rnateam
tool_panel_section_label: "RNA-Seq"
- name: data_manager_sortmerna_database_downloader
owner: rnateam
install_resolver_dependencies: false
# Conda package missing
#- name: blockclust
# owner: rnateam
# tool_panel_section_label: "RNA-Seq"
- name: flaimapper
owner: yhoogstrate
tool_panel_section_label: "RNA-Seq"
#- name: suite_mirdeep_2_0
# owner: rnateam
# tool_panel_section_label: "RNA-Seq"
# tool_shed_url: https://toolshed.g2.bx.psu.edu
# install_resolver_dependencies: True
# install_tool_dependencies: False
- name: pipmir
owner: rnateam
tool_panel_section_label: "RNA-Seq"
install_resolver_dependencies: false
- name: nastiseq
owner: rnateam
tool_panel_section_label: "RNA-Seq"
install_resolver_dependencies: false
- name: dr_disco
owner: erasmus-medical-center
tool_panel_section_label: "RNA-Seq"
# RNA Target Prediction
- name: targetfinder
owner: rnateam
tool_panel_section_label: "RNA Target Prediction"