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
  • Set up the Galaxy environment
  • Set up the de.STAIR tools
  • Run the Galaxy framework

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.

▲ back to top

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

▲ back to top

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

▲ back to top

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

▲ back to top