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Template:SeqShopExtSetup

2,449 bytes added, 16:15, 3 July 2014
Created page with "== Setup when running on your own outside of the SeqShop Workshop == ''This section is specifically for running on your own outside of the SeqShop Workshop.'' <div class="mw-c..."
== Setup when running on your own outside of the SeqShop Workshop ==
''This section is specifically for running on your own outside of the SeqShop Workshop.''
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''If you are running during the SeqShop Workshop, please skip this section.''
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=== Workshop Setup Steps ===
'''If this is your first SeqShop tutorial, you need to run some initial setup steps.'''

''These setup steps only need to be run once.''
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If you have already run another SeqShop tutorial, you can skip these steps (select 'Collapse' to hide the steps that you can skip)

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==== Download & Build GotCloud ====
* cd to where you want GotCloud installed (you can change this to any directory you want)
mkdir -p ~/seqshop
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/ - you will need to set the GC variable to the path.


==== Download the Workshop Example Data ====
wget http://www.sph.umich.edu/csg/mktrost/seqshopExample.tar.gz
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=== Setup your run environment ===

Environment variables will be used throughout the tutorial.

We recommend that you setup these variables so you won't have to modify every command in the tutorial.


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I'm using bash (replace the paths below with the appropriate paths):
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* Point to where you installed GotCloud
*:<pre>export GC=~/seqshop/gotcloud</pre>
* Point to where you installed the seqshop files
*:<pre>export SS=~/seqshop/example</pre>
* Point to where you want the output to go
*:<pre>export OUT=~/seqshop/output</pre>
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I'm using tcsh (replace the paths below with the appropriate paths):
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* Point to where you installed GotCloud
*:<pre>setenv GC ~/seqshop/gotcloud</pre>
* Point to where you installed the seqshop files
*:<pre>setenv SS ~/seqshop/example</pre>
* Point to where you want the output to go
*:<pre>setenv OUT ~/seqshop/output</pre>
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