Biowulf High Performance Computing at the NIH
Parpipe on NIH HPC Systems

PARpipe is a complete analysis pipeline for PAR-CLIP data providing the following features:

- Pre-processing and alignment of reads
- Definition of interaction sites using PARalyzer v1.5 (download)
- Additional site-level metrics
- Annotation of reads, groups, and cluster
- Meta-analysis of binding sites relative to important transcript features

Example files are under /usr/local/apps/parpipe/current/test directory.
To test with the example files:

  $ cp -r /usr/local/apps/parpipe/current/test /data/$USER
  $ cd /data/$USER/test
  $ sinteractive --mem=5g
  $ module load parpipe
  $ bpipe run -r /usr/local/apps/parpipe/current/ ./test.fastq

Index files are under


Batch job on Biowulf

Create a batch input file (e.g. For example:

module load parpipe

cd /data/$USER/dir
parpipe command 1
parpipe command 2

Then submit the file on biowulf

biowulf> $ sbatch

For more information regarding sbatch command :

Swarm of Jobs on Biowulf

Create a swarmfile (e.g. script.swarm). For example:

# this file is called script.swarm
cd dir1;parpipe command 1; parpipe command 2
cd dir2;parpipe command 1; parpipe command 2
cd dir3;parpipe command 1; parpipe command 2

Submit this job using the swarm command.

swarm -f script.swarm --module parpipe

For more information regarding swarm:

Interactive job on Biowulf

Allocate an interactive session. Sample session:

[user@biowulf ~]$ sinteractive --mem=5g
salloc.exe: Pending job allocation 15194042
salloc.exe: job 15194042 queued and waiting for resources
salloc.exe: job 15194042 has been allocated resources
salloc.exe: Granted job allocation 15194042
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn1719 are ready for job

[user@cn1719 ~]$ module load parpipe

[user@cn1719 ~]$ parpipe command