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Bioinformatics - RMAP

Instructions on how to run (and, if needed, install a customized version of) RMAP

RMAP maps reads from the next-generation sequencing technology.

  1. Running RMAP on Thunder
  2. Install customized RMAP on Thunder
Please refer to the CCAST User Guide and the the article Running Bioinformatics Software on HPC Clusters for general information about using CCAST resources and running bioinformatics software on CCAST's HPC clusters.

1. Running RMAP on Thunder

Example: Map shorts reads to a reference chromosome

Location: /mmfs1/thunder/projects/ccastest/training/examples/RMAP_example

File list

· rmap_job.pbs: job submission script 

· chr8.fasequences to be screened in fasta format


· Copy example directory to your SCRATCH directory

o    cp -r /mmfs1/thunder/projects/ccastest/training/examples/RMAP_example $SCRATCH

· Go to the copied directory

o    cd  $SCRATCH/RMAP_example

· Edit the job submission script as needed, then submit the job

o    qsub RMAP_job.pbs

2. Install Customized RMAP on Thunder

Warning: This part is intended ONLY for those who want to install and test their own version in their HOME directory.


(a) gcc version 4.1 or greater; (CCAST default gcc 4.8.5; module gcc 7.3.0) 

(b) Multi-core options not found. (In the test job status, the "resources_used.ncpus = 4", # of ncpus)


In the following pages, we assume that you want to install the software in a directory named “SOFTWARE” inside your HOME directory on the CCAST’s Thunder cluster. “USERNAME is your username on Thunder.

(a) Install

· Go to the SOFTWARE directory: 

o    "cd /mmfs1/home/USERNAME/SOFTWARE" 

· Git clone: (the file in has no test directory; notice the --recursive flag, for "rmap/src/utils" and "rmap/src/smithlab_cpp" are changed to submodules.)

o    "git clone --recursive" 

· Go to the rmap directory:  

o    "cd rmap"

· Install: (A 'bin' directory will be created in the current directory, and it will contain all the executables. These can be moved around, and do not depend on any dynamic libraries.)

o    "make install"

(b) Test

· Make a test directory and go into it: 

o    "cd /mmfs1/thunder/scratch/USERNAME " 

o    "mkdir RMAP_example"

o    "cd RMAP_example"

· Copy built-in test data to current location:  

o    "cp /gpfs1/home/USERNAME/SOFTWARE/rmap/test/input/{chr8.fa,test_reads.fa} .

· Write and submit the job 

o    "qsub rmap_job.pbs"

------------------------------------------- file rmap_job.pbs -------------------------------------------


#PBS -q default


#PBS -l select=1:mem=10gb:ncpus=4

#PBS -l walltime=02:00:00

## Replace “x-ccast-prj” with “x-ccast-prj-[your project group name here]”

#PBS -W group_list=x-ccast-prj




# Set path to your RMAP binaries

export MY_RMAP=/mmfs1/home/USERNAME/SOFTWARE/rmap/bin


$MY_RMAP/rmap -o test_reads.bed -a test_reads.amb -c ./ chr8.fa 

exit 0

See Also:

Keywords:ccast, hpc, thunder, bioinformatics, rmap   Doc ID:108079
Owner:Liu Y.Group:IT Knowledge Base
Created:2020-12-24 11:13 CSTUpdated:2022-08-09 08:23 CST
Sites:IT Knowledge Base
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