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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.
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: /gpfs1/projects/ccastest/training/examples/RMAP_example
File list
· rmap_job.pbs: job submission script
· chr8.fa: sequences to be screened in fasta format
Steps
· Copy example directory to your SCRATCH directory
o “cp -r /gpfs1/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.
Summary
(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)
Details
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 /gpfs1/home/USERNAME/SOFTWARE"
· Git clone: (the file in http://smithlabresearch.org/downloads/rmap-2.1.tar.bz2 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 https://github.com/smithlabcode/rmap.git"
· 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 /gpfs1/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 -------------------------------------------
#!/bin/bash
#PBS -q default
#PBS -N RMAP_Test
#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
cd $PBS_O_WORKDIR
# Set path to your RMAP binaries
export MY_RMAP=/gpfs1/home/USERNAME/SOFTWARE/rmap/bin
$MY_RMAP/rmap -o test_reads.bed -a test_reads.amb -c ./ chr8.fa
exit 0