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Revision as of 21:41, 10 December 2014
, 21:41, 10 December 2014→Setup in person at the SeqShop Workshop
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''If you are not already logged in, please expand this section.''
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{{SeqShopLogin}}
{{SeqShopLogin}}
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=== Setup your run environment===
=== Setup your run environment===
* Setup an output directory
* Setup an output directory
** It will leave your output directory from the previous tutorial in tact.
** It will leave your output directory from the previous tutorial in tact.
source /home/hmkang/seqshop/setup.txt
source /net/seqshop-server/home/hmkang/seqshop/setup.txt
* You won't see any output after running <code>source</code>
* You won't see any output after running <code>source</code>
** It silently sets up your environment
** It silently sets up your environment
** If you want to view the detail of the setup, type
** If you want to view the detail of the setup, type
less /home/mktrost/seqshop/setup.txt
less /net/seqshop-server/home/hmkang/seqshop/setup.txt
and press 'q' to finish.
and press 'q' to finish.
View setup.txt
View setup.txt
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export GC=/home/hmkang/seqshop/gotcloud
export GC=/net/seqshop-server/home/hmkang/seqshop/gotcloud
export IN=/home/hmkang/seqshop/inputs
export IN=/net/seqshop-server/home/hmkang/seqshop/inputs
export REF=/home/hmkang/seqshop/reference/chr22
export REF=/net/seqshop-server/home/hmkang/seqshop/reference/chr22
export VTREF=/home/hmkang/seqshop/reference/vtRef
export VTREF=/net/seqshop-server/home/hmkang/seqshop/reference/vtRef
export SV=/home/hmkang/seqshop/reference/svtoolkit
export SV=/net/seqshop-server/home/hmkang/seqshop/reference/svtoolkit
export EXT=/home/hmkang/seqshop/external
export EXT=/net/seqshop-server/home/hmkang/seqshop/external
export EPACTS=/home/hmkang/seqshop/epacts
export EPACTS=/net/seqshop-server/home/hmkang/seqshop/epacts
export OUT=~/out
export OUT=~/out
mkdir -p ${OUT}
mkdir -p ${OUT}
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== Setup when running on your own outside of the SeqShop Workshop ==
== Setup when running on your own outside of the SeqShop Workshop ==
