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Name

APPS/BIO/EXONERATE-2.2.0

Description

Exonerate sequence alignment tool.

Status

Production

Last update

2012-04-20

USAGE

Here is a simple test case for the runtime environment.

Download the example job here.

The job description file exonerate.xrsl

&
(executable=runexonerate.sh)
(jobname=exonerate)
(stdout=std_1.out)
(stderr=std_1.err)
(gmlog=gridlod_1)
(walltime=24h)
(memory=4000)
(runtimeenvironment>="APPS/BIO/EXONERATE-2.2.0")
(inputfiles=
( "seq1.fasta" "seq1.fasta" )
( "seq2.fasta" "seq2.fasta" )
)
(outputfiles=
  ( "result.out" "result.out" )
)

The job script runexonerate.sh is very simple

#!/bin/sh
echo "Hello exonerate"
exonerate seq1.fasta seq2.fasta > result.out
echo "Bye exonerate"
Commands to submit the sample job in linux and MacOSX machines

Download and unpack the sample job:

Set up grid environment and submit the job

arcproxy
arcsub exonerate.xrsl

Follow the progress of the job and retrieve the result when the job is finished,

arcstat job_id
arcget job_id

In the commands above, job_id should be replaced with the job identifier given by the the arcsub command for example:

arcstat gsiftp://grid.triton.aalto.fi:2811/jobs/2864513391466861182312366
arcget gsiftp://grid.triton.aalto.fi:2811/jobs/2864513391466861182312366

The arcget command will store the results of the job to a new directory named according to the job ID number.

Interface definition

The runtime environment sets the following environment variables:

  • PATH is set so that the installation directory of Exonerate binaries is included in the path

System administrator guide for installing the RE

Exonerate executables

Get and unload the package:

wget http://www.ebi.ac.uk/~guy/exonerate/exonerate-2.2.0-x86_64.tar.gz
tar zxvf exonerate-2.2.0-x86_64.tar.gz

Runtime environment

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/EXONERATE-2.2.0.

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

Contact information

Contact kimmo.mattila@csc.fi

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