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130 bytes added
, 09:39, 16 October 2014
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| * MOSIX | | * MOSIX |
| * SGE (Sun Grid Engine) | | * SGE (Sun Grid Engine) |
| + | ** Used by StarCluster |
| * SLURM | | * SLURM |
| + | * PBS (Portable Batch System) |
| | | |
| You can specify the type of cluster with the option '''-batchtype'''. In addition you can pass options | | You can specify the type of cluster with the option '''-batchtype'''. In addition you can pass options |
| to that cluster system with the option '''-batchopt'''. | | to that cluster system with the option '''-batchopt'''. |
| + | * Alternatively, you can set them using BATCH_TYPE and BATCH_OPTS in the configuration file. |
| For example, here are examples of invocations of the aligner using these batch systems: | | For example, here are examples of invocations of the aligner using these batch systems: |
| | | |
| <code> | | <code> |
− | '''gen_biopipeline.pl -conf ~/testalign.conf -out ~/outtest -batchtype slurm -batchopts "--mem 8g"''' | + | '''gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype slurm -batchopts "--mem 8g"''' |
| | | |
− | '''gen_biopipeline.pl -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-b"''' | + | '''gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-b"''' |
− | '''gen_biopipeline.pl -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-15,16,17"''' | + | '''gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-15,16,17"''' |
| | | |
− | '''gen_biopipeline.pl -conf ~/testalign.conf -out ~/outtest -batchtype sge''' | + | '''gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype sge''' |
| </code> | | </code> |
| | | |