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Revision as of 11:10, 26 June 2014
, 11:10, 26 June 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}
${GC}/gotcloud snpcall --conf ${SS}/gotcloud.conf --numjobs 4 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
* <code>${GC}/gotcloud</code> runs GotCloud
* <code>align</code> tells GotCloud you want to run the alignment pipeline.
* <code>--conf</code> tells GotCloud the name of the configuration file to use.
** The configuration for this test was downloaded with the seqshop input files.
* --numjobs tells GotCloud how many jobs to run in parallel
* --numjobs tells GotCloud how many jobs to run in parallel
** Depends on your system
** Depends on your system
* --region 22:36000000-37000000
* --region 22:36000000-37000000
** The sample files are just a small region of chromosome 22, so to save time, we tell GotCloud to ignore the other regions
** The sample files are just a small region of chromosome 22, so to save time, we tell GotCloud to ignore the other regions
* <code>--base_prefix</code> tells GotCloud the prefix to append to relative paths.
** The Configuration file cannot read environment variables, so we need to tell GotCloud the path to the input files, ${SS}
** Alternatively, gotcloud.conf could be updated to specify the full paths
* <code>--out_dir</code> tells GotCloud where to write the output.
** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line
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