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contributors:team_4_page [2015/05/11 08:39] emfeal [Running ABySS] |
contributors:team_4_page [2015/05/11 08:47] emfeal [Running ABySS] |
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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' | $ABYSSRUN np=10 k=21 name=ecoli in='/campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads1.fastq /campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads2.fastq' | ||
</code> | </code> | ||
- | Something to note is that using the parallel version of ABySS requires the use of a parallel environment which can be selected using a qsub option. The parallel environment option in the script above: | + | Note that the parallel version of ABySS requires two things in particular: |
+ | **(1)** the use of a parallel environment which can be selected using a qsub option. The parallel environment option in the script above: | ||
<code> | <code> | ||
#$ -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> |