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Setup when running on your own outside of the SeqShop Workshop
''If you are running during the SeqShop Workshop, please skip this section.''
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=== Download the example data ===
=== Setup your run environment === Environment variables will be used throughout This tutorial builds on the alignment tutorial. We recommend that you setup these variables so , if you won't have to modify every command in the not already, please first run that tutorial. <div class="mw-collapsible mw-collapsed" style="width:500px">I'm using bash (replace the paths below with the appropriate paths):<div class="mw-collapsible-content">* Point to where you installed GotCloud*:<pre>export GC=/home/username/gotcloud</pre>* Point to where you installed the seqshop files*:<pre>export SS=/home/username/seqshop/</pre>* Point to where you want the output to go*:<pre>export OUT=/home/username/seqshop_output/</pre></div></div> <div class="mw-collapsible mw-collapsed" style="width:500px">I'm using tcsh (replace the paths below with the appropriate paths):<div class="mw-collapsible-content">* Point to where you installed GotCloud*:<pre>setenv GC /home/username/gotcloud</pre>* Point to where you installed the seqshop files*:<pre>setenv SS /home/username/seqshop/</pre>* Point to where you want the output to go*[[SeqShop:<pre>setenv OUT /home/username/seqshop_output/</pre></div></div> </div></div>_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]]
{{SeqShopRemoteEnv}}
== Examining GotCloud SnpCall Input files ==

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