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, 17:19, 17 May 2015
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| ** How to evaluate the quality of SNP calls | | ** How to evaluate the quality of SNP calls |
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− | == Setup in person at the SeqShop Workshop == | + | == Setup == |
| ''This section is specifically for the SeqShop Workshop computers.'' | | ''This section is specifically for the SeqShop Workshop computers.'' |
− | <div class="mw-collapsible mw-collapsed" style="width:600px"> | + | <div class="mw-collapsible" style="width:600px"> |
| ''If you are not running during the SeqShop Workshop, please skip this section.'' | | ''If you are not running during the SeqShop Workshop, please skip this section.'' |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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| {{SeqShopLogin}} | | {{SeqShopLogin}} |
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− | === Setup your run environment===
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− | This is the same setup you did for the previous tutorial, but you need to redo it each time you log in.
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− | This will setup some environment variables to point you to
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− | * [[GotCloud]] program
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− | * Tutorial input files
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− | * Setup an output directory
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− | ** It will leave your output directory from the previous tutorial in tact.
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− | source /net/seqshop-server/home/mktrost/seqshop/setup.txt
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− | * You won't see any output after running <code>source</code>
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− | ** It silently sets up your environment
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− | ** If you want to view the detail of the setup, type
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− | less /net/seqshop-server/home/mktrost/seqshop/setup.txt
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− | and press 'q' to finish.
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− | <div class="mw-collapsible mw-collapsed" style="width:200px">
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− | View setup.txt
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− | <div class="mw-collapsible-content">
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− | [[File:setup.png|500px]]
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| </div> | | </div> |
| </div> | | </div> |
− | </div>
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− | </div>
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− | == Setup when running on your own outside of the SeqShop Workshop ==
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− | ''This section is specifically for running on your own outside of the SeqShop Workshop.''
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− | <div class="mw-collapsible" style="width:600px">
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− | ''If you are running during the SeqShop Workshop, please skip this section.''
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− | <div class="mw-collapsible-content">
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| 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]] | | 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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| {{SeqShopRemoteEnv}} | | {{SeqShopRemoteEnv}} |
− | </div>
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− | </div>
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| == Examining GotCloud SnpCall Input files == | | == Examining GotCloud SnpCall Input files == |