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some things you'll want to know about to make using GotCloud as simple to use as possible.
some things you'll want to know about to make using GotCloud as simple to use as possible.
'''Configure For Your Batch Environment'''
'''Configure Your Batch Environment'''
GotCloud supports two options to allow you to submit the work from the aligner and umake
GotCloud supports two options to allow you to submit the work from the aligner and umake
* 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>
