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--- contributors:team_4_page [2015/05/08 22:32]
sihussai
+++ contributors:team_4_page [2015/05/11 08:49]
emfeal [Running ABySS]
@@ Line 80: / Line 80: @@
 =====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 script. An example script which runs
+the parallel-version of ABySS on the cluster 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>
+Note that the parallel version of ABySS requires two things in particular: **(1)** the use of a parallel environment which can be selected using a qsub option.  The parallel environment option in the script above:
+<code>
+#$ -pe mpi 10
+</code>
+The //mpi// designates the choice of a parallel environment that is installed on the system and the 10 indicates the number of processes over which to run the job. To see which PE's are installed on the system, use the command:
+<code>
+qconf -spl
+</code>
+**(2)** the //np// option of abyss-pe. The number of processes here must reflect the number included in the parallel environment option.
 abyss-pe is a driver script implemented as a Makefile. Any option of make may be used with abyss-pe. Particularly useful options are:

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