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Revision as of 12:50, 3 July 2014
, 12:50, 3 July 2014→Getting started
export HGDP=/home/chaolong/LASER-Tutorial/HGDP
export HGDP=/home/chaolong/LASER-Tutorial/HGDP
export BAM=/home/chaolong/LASER-Tutorial/BAM
export BAM=/home/chaolong/LASER-Tutorial/BAM
== 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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=== Download the example data ===
=== 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=/home/username/gotcloud</pre>
* Point to where you installed the seqshop files
*:<pre>export SS=/home/username/seqshop/</pre>
* Point to where you want the output to go
*:<pre>export OUT=/home/username/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 /home/username/gotcloud</pre>
* Point to where you installed the seqshop files
*:<pre>setenv SS /home/username/seqshop/</pre>
* Point to where you want the output to go
*:<pre>setenv OUT /home/username/seqshop_output/</pre>
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== Preparing input files for LASER ==
== Preparing input files for LASER ==
