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--- contributors:team_4_page [2015/05/08 22:32]
sihussai
+++ contributors:team_4_page [2015/05/11 08:31]
emfeal [Running ABySS]
@@ Line 81: / Line 81: @@
 =====Running ABySS=====
+Running an assembly on the campusrocks cluster, which runs on SGE, requires the use of the qsub command.  The use of a shell script allows a convenient and concise way to wrap useful qsub options, environmental variable manipulations, and the executable (abyss-pe) itself in a single executable script. An example script which runs
+the parallel-version of ABySS is shown below.
+<code>
+#!/bin/sh
+#
+#$ -N team4
+#$ -cwd
+#$ -j y
+#$ -pe mpi 10
+#$ -S /bin/bash
+#$ -V
+#$ -l mem_free=15g
+#
+ABYSSRUNDIR=/campusdata/BME235/bin
+export PATH=$PATH:/opt/openmpi/bin:/campusdata/BME235/bin/
+export LD_LIBRARY_PATH=/opt/openmpi/lib/:$LD_LIBRARY_PATH
+ABYSSRUN=$ABYSSRUNDIR/abyss-pe
+$ABYSSRUN np=10 k=21 name=ecoli in='/campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads1.fastq /campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads2.fastq'
+</code>
+A qsub option of import which is vital to successfully run a parallel ABySS job on the cluster is the use of a parallel environment. The PE designated in the script above:
+<code>
+#$ -pe mpi 10
+</code>
+The //-pe// designates the parallel environment qsub option.  The //mpi// designates the choice of a parallel environment that is installed on the system. The 10 indicates the number of processes you wish the job to be parallelized over. To see which PE's are installed on the system, use the command:
+<code>
+qconf -spl
+</code>
 abyss-pe is a driver script implemented as a Makefile. Any option of make may be used with abyss-pe. Particularly useful options are:
 <code>

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