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Jump to navigationJump to search→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.
You must specify the <code>--conf</code> parameter followed by the configuration file to be used for this run of the alignment pipeline.
gotcloud align --outdir ~/gotcloudOutput/align/ --conf myAlignTest.conf
If your configuration file does not contain an output directory, you must specify <code>--outdir</code> on the command-line to tell the alignment pipeline where to write its output.
'''Example of a Basic Alignment Command'''
gotcloud align --conf myAlignTest.conf --outdir ~/gotcloudOutput/align/
