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Revision as of 14:32, 21 November 2014
, 14:32, 21 November 2014→Run GotCloud Align
Now that we have all of our input files, we need just a simple command to run them
Now that we have all of our input files, we need just a simple command to run them
${GC}/gotcloud align --conf ${SS}/gotcloud.conf --numcs 2 --base_prefix ${SS} --outdir ${OUT}
${GC}/gotcloud align --conf ${SS}/gotcloud.conf --numjobs 2 --base_prefix ${SS} --outdir ${OUT}
* <code>${GC}/gotcloud</code> runs GotCloud
* <code>${GC}/gotcloud</code> runs GotCloud
* <code>--conf</code> tells GotCloud the name of the configuration file to use.
* <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.
** The configuration for this test was downloaded with the seqshop input files.
* <code>--numcs</code> means to run 2 samples at a time.
* <code>--numjobs</code> means to run 2 samples at a time.
** How many you can run concurrently depends on your system.
** How many you can run concurrently depends on your system.
* <code>--base_prefix</code> tells GotCloud the prefix to append to relative paths.
* <code>--base_prefix</code> tells GotCloud the prefix to append to relative paths.
