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Revision as of 14:21, 3 July 2014
, 14:21, 3 July 2014→Setup when running on your own outside of the SeqShop Workshop
''If you are running during the SeqShop Workshop, please skip this section.''
''If you are running during the SeqShop Workshop, please skip this section.''
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=== Download & Build GotCloud ===
If you do not already have GotCloud:
* cd to where you want GotCloud installed (you can change this to any directory you want)
cd ~/seqshop/
* download, decompress, and build the version of gotcloud that was tested with this tutorial:
wget https://github.com/statgen/gotcloud/archive/gotcloud.workshop.tar.gz
tar xvf gotcloud.workshop.tar.gz
mv gotcloud-gotcloud.workshop gotcloud
cd gotcloud/src
make
cd ../..
Remember the path to gotcloud/ that is what you will need to set your GC variable to.
=== Download the example data ===
=== Download the example data ===
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* Point to where you installed GotCloud
* Point to where you installed GotCloud
*:<pre>export GC=/home/username/gotcloud</pre>
*:<pre>export GC=~/seqshop/gotcloud</pre>
* Point to where you installed the seqshop files
* Point to where you installed the seqshop files
*:<pre>export SS=/home/username/seqshop/</pre>
*:<pre>export SS=~/seqshop/example</pre>
* Point to where you want the output to go
* Point to where you want the output to go
*:<pre>export OUT=/home/username/seqshop_output/</pre>
*:<pre>export OUT=~/seqshop/output</pre>
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* Point to where you installed GotCloud
* Point to where you installed GotCloud
*:<pre>setenv GC /home/username/gotcloud</pre>
*:<pre>setenv GC ~/seqshop/gotcloud</pre>
* Point to where you installed the seqshop files
* Point to where you installed the seqshop files
*:<pre>setenv SS /home/username/seqshop/</pre>
*:<pre>setenv SS ~/seqshop/example</pre>
* Point to where you want the output to go
* Point to where you want the output to go
*:<pre>setenv OUT /home/username/seqshop_output/</pre>
*:<pre>setenv OUT ~/seqshop/output</pre>
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