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Revision as of 15:48, 10 July 2014
, 15:48, 10 July 2014→GotCloud BAM Index File
;Do you notice a difference between this index and yours?
;Do you notice a difference between this index and yours?
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<li>Answer:</li>
<li>Answer:</li>
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<li>It doesn't have a full path to the BAM file, while your index has /home/...</li>
<li>It doesn't have a full path to the BAM file, while your index has /home/...</li>
[[File:Bamindex1.png|300px]]
[[File:Bamindex1.png|300px]]
<li>That's ok, <code>gotcloud.conf</code> contains the path to those BAMs</li>
<li>That's ok, we will use the <code>--base_prefix ${SS}</code> command-line option to prefix the BAM paths</li>
<li>Alternatively, we could have set BAM_INDEX in <code>gotcloud.conf</code> to the path to the BAMs
<pre>BAM_INDEX = /home/username/seqshop/example</pre> </li>
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<li>NOTE: the conf file can't interpret ${SS} environment variables or '~', so you would have to specify the full path</li>
<li>We just used the command-line option for this tutorial since this path will vary by user.</li>
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