Bowtie2 through rcbio

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

mkdir /n/scratch/users/a/abc123/bowtie2
cd  /n/scratch/users/a/abc123/bowtie2

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

Clone rcbio, setup path and copy the example bowtie2 bash script:

# This will setup the path and environment variables for the pipeline
git clone https://github.com/ld32/rcbio.git $HOME/rcbio
export PATH=$HOME/rcbio/bin:$PATH

cp $HOME/rcbio/bin/bowtie2.sh .

Now you can modify the options as needed. Please reference the bowtie2 user manual if you have any questions.

To edit the Kallisto and Sleuth bash script:

nano bowtie2.sh

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

runAsPipeline "bowtie2.sh -r dm3" "sbatch -p short --mem 6G -t 2:0:0 -n 1" useTmp


# this is a test run

To run the pipeline:

runAsPipeline "bowtie2.sh -r dm3" "sbatch -p short --mem 6G -t 2:0:0 -n 1" useTmp 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

Now you are ready to run an rcbio workflow

To instead run the workflow on your own data, transfer the sample sheet to your local machine following this wiki page and modify the sample sheet. Then you can transfer it back to O2 under your account, then go to the build folder structure step.