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)>