SHRiMP Runtime Environment home page

Version information

Only this development version currently available.

Interface definition

The runtime environment sets the following environment variables:

• SHRIMP_DIR points to the SHRIMP/bin base directory
• PATH is set so that the $SHRIMP_DIR is included in the path
• SHRIMPDB is set to a suitable temporary directory for unpacking the datasets
• SHRIMP_NUM_CPUS is set to the number of allocated cpus for this job. Remember to use option: -N $SHRIMP_NUM_CPUS ... when running.

Examples

Here is a simple test case for the runtime environment.

Download the example files here.

The job description file bwa.xrsl

&
(executable=runshrimp.sh)
(jobname=bwa_1)
(stdout=std_1.out)
(stderr=std_1.err)
(gmlog=gridlog_1)
(walltime=24h)
(memory=8000)
(disk=4000)
(runtimeenvironment>="APPS/BIO/SHRIMP_2.2.2")
(inputfiles=
( "query.fastq" "query.fastq" )
( "S_pyogenes_m2.EB1_s_pyogenes_m2.dna.toplevel.fa" "S_pyogenes_m2.EB1_s_pyogenes_m2.dna.toplevel.fa" )
)
(outputfiles=
  ( "output.sam" "output.sam" )
)

The job script, runshrimp.sh is very simple

#!/bin/sh
echo "Hello SHRiMP!"
genome="S_pyogenes_m2.EB1_s_pyogenes_m2.dna.toplevel.fa"
query="query.fasta"
gmapper-ls $query -L $genome > output.sam 
exitcode=$?
echo "Bye SHRiMP!"
exit $exitcode

Here the actual run consists of just on command that maps the query sequences against the reference genome. The exitcode from gmapper-ls is used as the exit code for the script, this way ARC knows whether the job has succeeded or failed.

System administrator guide for installing the RE

SHRiMP source code

Source and installation instructions for the SHRiMP software itself can be found from the SHRiMP home page The easiest way to install SHRiMP is to download a suitable pre-compiled version of the program from the SHRiMP home page.

Download runtime environment script template for SLURM.

Modify the scripts as needed and save the main script in your ARC runtime directory as APPS/BIO/SHRIMP_2.2.2. If you wish to use the grid_bwa submission tool, make sure that you have also SAMTOOLS run time environemnt installed in your cluster.

As long as the interface requirements are satisfied, the implementation does not really matter. And some adaptation is needed anyway to accomondate differences in the cluster environment (batch queue systems, temporary directory location etc.)

Contact information

Contact kimmo.mattila@csc.fi if you have any grid_bwa use specific questions. Contact your local SHRiMP guru in sequence analysis related questions.