Workflow

https://www.lucidchart.com/documents/view/6a805a1f-7d82-43cf-b0a4-4e71faed9ce1

Instructions

Step 0: get the pipeline

git clone https://github.com/CCBR/RNASeqPipeline

Step 1: login mode

1/ add a BASH_ENV to your .bashrc file

1-1 Create a file called ~/.bash_script_exports. The contents of the file should be: source /usr/local/Modules/default/init/bash

1-2 Add to your /.bashrc file this line: export BASH_ENV=/.bash_script_exports

2/ allow X11 display

• login with option -X example: ssh -X [email protected]

Step 2: data, config and scripts

3/ cp *.sh path2workingdirectory

4/ cp *.json path2workingdirectory

edit the config file & rename it config.json

Step 3: run pipeline from your working directory

test and check your configuration (fake run)

5/ bash dryrun.sh

main call (real run)

6/ qsub -V -l nodes=1:gpfs submit.sh