Tools¶
This repository contains the de.STAIR tools that are incorporated in the Galaxy workflow generator, to assist users in the analysis of RNA-Seq and BS/RRBS-Seq data.
How to contribute¶
Tools can be tested, modified, and extended. The following sections will help you set up the Galaxy framework to contribute to the tools.
Set up the Galaxy environment¶
Create a directory for the Galaxy repository
$ export GALAXY_ROOT=/path/to/galaxy
Clone the Galaxy repository into the directory
$ git clone https://github.com/galaxyproject/galaxy.git $GALAXY_ROOT
Enter in the Galaxy repository, and checkout version 19.01
$ cd $GALAXY_ROOT
$ git checkout v19.01
Set up the de.STAIR tools¶
Create a directory for the de.STAIR Galaxy tools repository
$ export DESTAIR_GALAXY_TOOLS=/path/to/destair-galaxy-tools
Clone the de.STAIR Galaxy tools repository
$ git clone https://github.com/destairdenbi/galaxy-tools.git $DESTAIR_GALAXY_TOOLS
Set up the de.STAIR tools into the cloned Galaxy repository
$ $DESTAIR_GALAXY_TOOLS/setup.sh
Run the Galaxy framework¶
Run the Galaxy launch script to verify the Galaxy framework setup and the inclusion of the new tools
$ $GALAX_ROOT/run.sh