contributors:team_4_page
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| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
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contributors:team_4_page [2015/05/11 08:49] emfeal [Running ABySS] |
contributors:team_4_page [2015/05/11 08:56] 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' | $ABYSSRUN np=10 k=21 name=ecoli in='/campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads1.fastq /campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads2.fastq' | ||
| </code> | </code> | ||
| - | Note that the parallel version of ABySS requires two things in particular: **(1)** the use of a parallel environment which can be selected using a qsub option. The parallel environment option in the script above: | + | Note that the parallel version of ABySS requires two things in particular: |
| + | - The use of a parallel environment which can be selected using a qsub option. The parallel environment option in the script above: | ||
| <code> | <code> | ||
| #$ -pe mpi 10 | #$ -pe mpi 10 | ||
| Line 106: | Line 107: | ||
| 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. | + | - 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: | ||
contributors/team_4_page.txt · Last modified: 2015/07/18 20:52 by 92.247.181.31
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