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Revision as of 19:46, 7 December 2014
, 19:46, 7 December 2014→GotCloud BAM List File
<li>That's ok, we will use the <code>--base_prefix ${SS}</code> command-line option to prefix the BAM paths</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_PREFIX in <code>gotcloud.conf</code> to the path to the BAMs
<li>Alternatively, we could have set BAM_PREFIX in <code>gotcloud.conf</code> to the path to the BAMs
<pre>BAM_PREFIX = /home/username/seqshop/example</pre> </li>
<pre>BAM_PREFIX = /net/seqshop-server/home/mktrost/seqshop/example</pre> </li>
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<ul>
<li>NOTE: the conf file can't interpret ${SS} environment variables or '~', so you would have to specify the full path</li>
<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>
<li>We just used the command-line option for this tutorial since this path will vary by user when running outside the workshop.</li>
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</ul>
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