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Methylflow on Biowulf & Helix


Cell-specific methylation pattern reconstruction. Currently uses an LP formulation and solver. The lemon graph library http://lemon.cs.elte.hu/trac/lemon and the glpk LP solver http://www.gnu.org/software/glpk/ are included in this repository. The ezOptionParser.hpp is also included http://ezoptionparser.sourceforge.net/

The algorithm is described and tested in this publication: http://bioinformatics.oxfordjournals.org/content/32/11/1618.abstract

There may be multiple versions available on our systems. An easy way of selecting the version is to use modules. To see the modules available, type

module avail methylflow 

To select a module use

module load methylflow/[version]

where [version] is the version of choice.

Environment variables set


Interactive Job on Biowulf

Allocate an interactive session with sinteractive and use as described below

biowulf$ sinteractive --mem=5g
salloc.exe: Pending job allocation 38978697
salloc.exe: Nodes cn2273 are ready for job
node$ module load methylflow
[+] Loading methylflow
node$ methylFlow -sam -i reads.sam -o mfoutput -l 10.0 -s 30.0 -e 0.1
node$ exit


Batch job on Biowulf

Create a batch script similar to the following example:

#! /bin/bash
# this file is file.batch

module load methylflow || exit 1
cd /data/$USER
methylFlow -sam -i reads.sam -o mfoutput -l 10.0 -s 30.0 -e 0.1

Submit to the queue with sbatch:

biowulf$ sbatch file.batch


Swarm of Jobs on Biowulf

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

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

Submit this job using the swarm command.

swarm -f script.swarm --module methylflow

For more information regarding swarm: https://hpc.nih.gov/apps/swarm.html#usage