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Revision as of 14:04, 21 May 2015
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This tutorial builds on the alignment & snpcall tutorials, if you have not already, please first run those tutorials: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]] & [[SeqShop: Variant Calling and Filtering for SNPs Practical|SNP Calling Tutorial]]
This tutorial builds on the alignment & snpcall tutorials, if you have not already, please first run those tutorials: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]] & [[SeqShop: Variant Calling and Filtering for SNPs Practical|SNP Calling Tutorial]]
=== Download & Build EPACTS ===
=== Download & Build EPACTS ===
If you do not already have EPACTS:
If you do not already have EPACTS:
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''If you are running during the SeqShop Workshop, please skip this section and use EPACTS from Mary Kate's directory.''
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* cd to where you want EPACTS installed (you can change this to any directory you want)
* cd to where you want EPACTS installed (you can change this to any directory you want)
mkdir -p ~/seqshop
mkdir -p ~/seqshop
make install
make install
cd ../..
cd ../..
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{{SeqShopRemoteEnv}}
{{SeqShopRemoteEnv}}
<li>Using bash (replace the paths below with the appropriate paths):</li>
<li>Using bash (replace the paths below with the appropriate paths):</li>
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:<pre>export EPACTS=~/seqshop/epacts</pre>
:<pre>export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts</pre>
:<pre>export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts</pre>
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