galaxy-mytools_setup

====

Overview

Setup ENV for Execute BiT-Workflow (RNA seq + DEG)

###1. downsize_fastq_script(Dir)

• downsize fastq-files.

  • /downsize_fastq.sh

    • use: $sh downsize_fastq.sh <fastq_dir-path> <downsize(ex:1/10 = 10)>

  • /listQuartz.txt

    • to define the list of file to downsize（not need ".fastq"）

###2. install_toolshed_tools(Dir)

• install stable toolShed-Tools to Galaxy.

  • /install_toolshed_tools.py

    • use: python install_toolshed_tools.py <galaxy username(admin)>

  • /tool_shed_tool_list.yaml

    • to define a list of tools and their versions that will be installed as Galaxy.

###3. setup_reference_and_index(Dir)

• create sailfish index and transcriptome.fa setting for RNA-seq to be used Galaxy.

• Requirement: Galaxy Master API_KEY (setting ini)

  • /setup_TranscriptomeRef_in_Galaxy.py

    • use: python setup_TranscriptomeRef_in_Galaxy.py <Ref file_list.txt> <galaxy username(admin)>

  • /setup_sailfish_in_Galaxy.py

    • use: python setup_sailfish_in_Galaxy.py <Ref file_list.txt> <galaxy username(admin)>

  • /index_file_list.txt

    • to define a list of Reference Seqence files information.

###4. bit-tools_install.py

• clone, install and setting BiT custom-tools.

• Requirement: remove, move or rename dir "..galaxy_dist/tools/galaxy-mytools_rnaseq" before script execute.

• use: python bit-tools_install.py <galaxy username(admin)>

###5. bit-workflow_install.py

• clone, install and setting BiT custom-WFs.

• Requirement: remove, move or rename dir "..galaxy_dist/workflow_file/galaxy-workflow_rnaseq" before script execute.

• use: python bit-tools_install.py <galaxy username(admin)>

License (MIT)

Copyright (c) 2015 Mika Yoshimura and RIKEN Bioinformatics Research Unit Released under the MIT license (http://www.opensource.org/licenses/mit-license.php)