SAMtools Runtime Environment home page

Version information

Only this development version currently available.

Interface definition

The runtime environment sets the following environment variables:

• SAMTOOLS_DIR points to the samtools/bin base directory
• PATH is set so that the $SAMTOOLS_DIR is included in the path

Examples

Here is a simple test case for the runtime environment.

Download the example files here.

The job description file samtools.xrsl

&
(executable=runsamtools.sh)
(jobname=bwa_1)
(stdout=std_1.out)
(stderr=std_1.err)
(gmlog=gridlog_1)
(walltime=2h)
(memory=8000)
(disk=4000)
(runtimeenvironment>="APPS/BIO/SAMTOOLS")
(inputfiles=
( "input.sam" "input.sam" )
)
(outputfiles=
  ( "output.bam" "output.bam" )
  ( "output.bam.bai" "output.bam.bai" )
)

The job script runsamtools.sh is very simple

#!/bin/sh
echo "Hello SAMtools!"
input="input.sam"
output="output"
samtools view -S $input -b > converted.bam
samtools sort converted.bam $output
samtools index "$output".bam
exitcode=$?
echo "Bye SAMtools!"
exit $exitcode

Here the actual run consists of three steps: 1. Converting SAM formatted file into BAM format (samtools view), 2. Sorting the BAM formatted file (samtools sort), 3. Indexing the sorted BAM file (samtools index). The exitcode from samtools index 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

SAMtools source code

Source and installation instructions for the SAMtools software itself can be found from the SAMtools home page

Here is an example of installing the 0.1.18 version of SAMtools.

Get the package:

wget http://downloads.sourceforge.net/project/samtools/samtools/0.1.18/samtools-0.1.18.tar.bz2
bunzip2 samtools-0.1.18.tar.bz2 
tar xvf samtools-0.1.18.tar

And compile:

cd samtools-0.1.18
make

Finally, copy the executables to a bin directory

mkdir bin
mv samtools bin/
mv bcftools/bcftools bin/
cp misc/* bin/
rm bin/*.c bin/*.o bin/Makefile

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/SAMTOOLS.

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 SAMtools guru in sequence analysis related questions.