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Revision as of 17:49, 19 October 2014
, 17:49, 19 October 2014→Running the GotCloud Alignment Pipeline
The alignment pipeline is run using the <code>align</code> option of the <code>gotcloud</code> script. This option calls <code>align.pl</code> found in the <code>bin/</code> directory under the <code>gotcloud</code> installation.
The alignment pipeline is run using the <code>align</code> option of the <code>gotcloud</code> script. This option calls <code>align.pl</code> found in the <code>bin/</code> directory under the <code>gotcloud</code> installation.
Use the <code>--conf</code> parameter followed by the configuration file to specify the configuration to use for this run of the alignment pipeline.
You must specify the input list of FASTQs mapped to sample id to tell the alignment pipeline what files to process. You can do this by setting either:
* <code>FASTQ_LIST</code> in the configuration file
* <code>--list</code> on the command-line
You must specify an output directory to tell the alignment pipeline where to write its output by either setting:
* <code>OUT_DIR</code> in the configuration file
* <code>--outdir</code> on the command-line
'''Example of a Basic Alignment Command'''
'''Example of a Basic Alignment Command'''
If you see "Successfully ran the test case, congratulations!", then you are ready to align samples.
If you see "Successfully ran the test case, congratulations!", then you are ready to align samples.
== Input Data:==
== Input Data:==
