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, 10:59, 9 July 2014
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| | ''If you are running during the SeqShop Workshop, please skip this section.'' | | ''If you are running during the SeqShop Workshop, please skip this section.'' |
| | <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
| − | === Download the example data ===
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| − | === Setup your run environment ===
| + | This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]] |
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| − | Environment variables will be used throughout the tutorial.
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| − | | |
| − | We recommend that you setup these variables so you won't have to modify every command in the tutorial.
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| − | <div class="mw-collapsible mw-collapsed" style="width:500px">
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| − | I'm using bash (replace the paths below with the appropriate paths):
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| − | <div class="mw-collapsible-content">
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| − | * Point to where you installed GotCloud
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| − | *:<pre>export GC=/home/username/gotcloud</pre>
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| − | * Point to where you installed the seqshop files
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| − | *:<pre>export SS=/home/username/seqshop/</pre>
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| − | * Point to where you want the output to go
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| − | *:<pre>export OUT=/home/username/seqshop_output/</pre>
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| − | </div>
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| − | </div>
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| − | <div class="mw-collapsible mw-collapsed" style="width:500px">
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| − | I'm using tcsh (replace the paths below with the appropriate paths):
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| − | <div class="mw-collapsible-content">
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| − | * Point to where you installed GotCloud
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| − | *:<pre>setenv GC /home/username/gotcloud</pre>
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| − | * Point to where you installed the seqshop files
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| − | *:<pre>setenv SS /home/username/seqshop/</pre>
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| − | * Point to where you want the output to go
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| − | *:<pre>setenv OUT /home/username/seqshop_output/</pre>
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| − | </div>
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| − | </div>
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| − | | |
| − | </div>
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| − | </div>
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| | + | {{SeqShopRemoteEnv}} |
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| | == Examining GotCloud SnpCall Input files == | | == Examining GotCloud SnpCall Input files == |
