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coltron

Package for generating and analyzing transcription networks

Installation of Coltron has only been vetted on Ubuntu 12.04 LTS and Ubuntu 14.04 LTS. If you encounter any errors, please contact drpolaskijr@gmail.com for additional help.

Web site
Reference

coltron On Helix
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coltron requires several input files and the name and location for output. (User input in bold)

[user@helix ~]$ module load coltron
[+] Loading coltron 1.0.2 on biowulf.nih.gov
[+] Loading gcc 4.7.4 ...
[+] Loading bamliquidator version 1.3...
[+] Loading samtools 1.3.1 ...
[+] Loading openmpi 1.8.4 for GCC 4.4.7

[user@helix ~]$ coltron -e enhancer.table.txt -b file.bam -g genome.fa -o outputfile -n jobname

Running a single coltron job on Biowulf
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Set up a batch script along the following lines:

#!/bin/bash
# file called myjob.bat

cd /path/to/data
module load coltron 
coltron -e enhancer.table.txt -b file.bam -g genome.fa -o outputfile -n jobname

Submit this job with:

[user@biowulf ~]$ sbatch myjob.bat

For more information on submitting jobs to slurm, see Job Submission in the Biowulf User Guide.

Running a swarm of coltron jobs on Biowulf
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Set up a swarm command file containing one line for each of your coltron runs.

Sample swarm command file

# --------file myjobs.swarm----------
coltron -e enhancer.table.txt -b file1.bam -g genome.fa -o outputfile -n jobname
coltron -e enhancer.table.txt -b file2.bam -g genome.fa -o outputfile -n jobname
coltron -e enhancer.table.txt -b file3.bam -g genome.fa -o outputfile -n jobname
....
coltron -e enhancer.table.txt -b fileN.bam -g genome.fa -o outputfile -n jobname
# -----------------------------------

Submit this set of runs to the batch system by typing

[user@biowulf ~]$ swarm --module coltron -f myjobs.swarm

For details on using swarm see Swarm on Biowulf.

Documentation
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The source code for coltron can be found here. A minimal usage document can also be printed by typing coltron without options or arguments in the shell.