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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.
===Simple Example Alignment Command===
gotcloud align --outdir ~/gotcloudOutput/align/ --conf myAlignTest.conf
===Running the Automated Test===
===Running the Automated Test===
where OUTPUT_DIR is the directory where you want to store the test results
where OUTPUT_DIR is the directory where you want to store the test results
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.
== Overview of Alignment Pipeline Steps ==
== Overview of Alignment Pipeline Steps ==
