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Start an interactive job, with a walltime of 2 hours, 2000MB of memory. 

srun --pty -p interactive -t 0-02:0:0 --mem 2000MB -n 1 /bin/bash

Create a working directory on scratch3 scratch and change into the newly-created directory. For example, for user abc123, the working directory will be

mkdir /n/

scratch/users/a/abc123/skewerFastQCHisat2StringtieBallgown
cd  /n/

scratch/users/a/abc123/skewerFastQCHisat2StringtieBallgown

Copy some test data following this page: Build Folder Structures From Sample Sheet for rcbio NGS Workflows

Load necessary modules: 

module load gcc/6.2.0 python/2.7.12 rcbio/1.3.3

Copy the example skewerFastQCHisat2StringtieBallgown.sh bash script, and the ballgown.r R code:

cp /n/app/rcbio/1.3.3/bin/skewerFastQCHisat2StringtieBallgown.sh /n/app/rcbio/1.1/bin/ballgown.r .

Now you can modify the options as needed. For example, if you have single end data, you should add read length. Please reference the Hisat2 user manual if you have any questions.

To edit the Kallisto and Sleuth bash script:

nano skewerFastQCHisat2StringtieBallgown.sh
 
 
nano ballgown.r

To test the pipeline run the following command. Jobs will not be submitted to the scheduler.

runAsPipeline "skewerFastQCHisat2StringtieBallgown.sh -r mm10 -a /home/ld32/rcbioDev/data/skewer_adapters.fa"   "sbatch -p short -t 2:0:0 -n 1 --mem 4G" noTmp
 
 
# this is test run

To run the pipeline:

runAsPipeline "skewerFastQCHisat2StringtieBallgown.sh -r mm10 -a /home/ld32/rcbioDev/data/skewer_adapters.fa"   "sbatch -p short -t 2:0:0 -n 1 --mem 4G" noTmp run 2>&1 | tee output.log
 
 
# notice here 'run 2>&1 | tee output.log' is added to the command

To understand how 'runAsPipeline' works, how to check output, how to re-run the pipeline, please visit: Run Bash Script As Slurm Pipeline

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