contributors:team_4_page
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contributors:team_4_page [2015/06/02 00:38] emfeal [Installing ABySS] |
contributors:team_4_page [2015/07/18 20:31] ceisenhart ↷ Links adapted because of a move operation |
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| </code> | </code> | ||
| ==== Notes on Installation ==== | ==== Notes on Installation ==== | ||
| - | * the //-enable-maxk// is by default set to 64. Always ensure to set the max kmer is set to the smallest possible value that accommodates your target kmers so as to minimize ABySS's memory footprint. | + | * the //-enable-maxk// is by default set to 64. Always ensure the max kmer is set to the smallest possible value that accommodates your target kmers so as to minimize ABySS's memory footprint. |
| * ensure that the CPPFLAGS specified directory holds the google sparsehash includes. Look for a warning in the ABySS compilation to be sure. | * ensure that the CPPFLAGS specified directory holds the google sparsehash includes. Look for a warning in the ABySS compilation to be sure. | ||
| * the boost libraries do not need to be compiled before installing. | * the boost libraries do not need to be compiled before installing. | ||
| Line 103: | Line 103: | ||
| </code> | </code> | ||
| Note that the parallel version of ABySS requires two things in particular: | Note that the parallel version of ABySS requires two things in particular: | ||
| - | * The use of a [[parallel environment]] (PE) which can be selected using a qsub option. | + | * The use of a [[:parallel_environment]] (PE) which can be selected using a qsub option. |
| * 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. | ||
| The PE option in the script above: | The PE option in the script above: | ||
contributors/team_4_page.txt · Last modified: 2015/07/18 20:52 by 92.247.181.31
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