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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/parclip_pipe.sh ./test.fastq

On Helix

Sample session:

[helix ~]$ module load parpipe
[helix ~]$ bpipe run -r /usr/local/apps/parpipe/current/parclip_pipe.sh ./test.fastq

Batch job on Biowulf

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

module load parpipe

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

Then submit the file on biowulf

biowulf> $ sbatch script.sh

For more information regarding sbatch command : https://hpc.nih.gov/docs/userguide.html#submit

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: https://hpc.nih.gov/apps/swarm.html#usage

Interactive job on Biowulf

Allocate an interactive session. Sample session:

[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

[cn1719 ~]$ module load parpipe

[cn1719 ~]$ parpipe command