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Revision as of 17:24, 25 June 2014
, 17:24, 25 June 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 ${IN}/gotcloud.conf --numcs 2
${GC}/gotcloud align --conf ${SS}/gotcloud.conf --numcs 2 --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.
* <code>--numcs</code> means to run 2 samples at a time.
* <code>--numcs</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.
[[File:gcalignStart.png|850px]]
* <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.[[File:gcalignStart.png|850px]]
** 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
This should take 1-3 minutes to run.
This should take 1-3 minutes to run.
