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| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
| | | |
| + | <div class="mw-collapsible mw-collapsed" style="width:600px"> |
| + | ''If you are not already logged in, please expand this section.'' |
| + | <div class="mw-collapsible-content"> |
| {{SeqShopLogin}} | | {{SeqShopLogin}} |
| + | </div> |
| + | </div> |
| | | |
| === Setup your run environment=== | | === Setup your run environment=== |
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| * 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. |
| | | |
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| View setup.txt | | View setup.txt |
| <div class="mw-collapsible-content" style="width:800px"> | | <div class="mw-collapsible-content" style="width:800px"> |
− | 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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| </div> | | </div> |
| </div> | | </div> |
− |
| |
| | | |
| == Setup when running on your own outside of the SeqShop Workshop == | | == Setup when running on your own outside of the SeqShop Workshop == |