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Revision as of 19:54, 7 December 2014
, 19:54, 7 December 2014→Run GotCloud SnpCall
Now that we have all of our input files, we need just a simple command to run:
Now that we have all of our input files, we need just a simple command to run:
${GC}/gotcloud snpcall --conf ${SS}/gotcloud.conf --numjobs 4 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
* When running at home if you don't have 6 CPUs, reduce the --numjobs setting (it will take longer to run).
${GC}/gotcloud snpcall --conf ${SS}/gotcloud.conf --numjobs 6 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
* <code>${GC}/gotcloud</code> runs GotCloud
* <code>${GC}/gotcloud</code> runs GotCloud
* <code>align</code> tells GotCloud you want to run the alignment pipeline.
* <code>align</code> tells GotCloud you want to run the alignment pipeline.
