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contributors:team_4_page [2015/05/11 08:37] emfeal [Running ABySS] |
contributors:team_4_page [2015/05/11 08:47] emfeal [Running ABySS] |
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=====Running ABySS===== | =====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 | + | 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 is shown below. | + | the parallel-version of ABySS on the cluster is shown below. |
<code> | <code> | ||
#!/bin/sh | #!/bin/sh | ||
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$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' | $ABYSSRUN np=10 k=21 name=ecoli in='/campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads1.fastq /campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads2.fastq' | ||
</code> | </code> | ||
- | Something to note is that using the parallel version of ABySS on the cluster requires the use of a parallel environment which can be selected using a qsub option. The parallel environment option in the script above: | + | Note that the parallel version of ABySS requires two things in particular: |
+ | **(1)** the use of a parallel environment which can be selected using a qsub option. The parallel environment option in the script above: | ||
<code> | <code> | ||
#$ -pe mpi 10 | #$ -pe mpi 10 | ||
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qconf -spl | qconf -spl | ||
</code> | </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: | 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> | <code> |