Changes

From Genome Analysis Wiki
Jump to navigationJump to search

SeqShop: Estimates of Genetic Ancestry Practical, June 2014 (view source)

Revision as of 09:40, 10 July 2014

780 bytes removed ,  09:40, 10 July 2014
no edit summary
Line 54: Line 54:     
{{SeqShopRemoteEnv}}
 
{{SeqShopRemoteEnv}}
−
</div>
  −
</div>
  −
  −
=== 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.
      +
<ul>
 +
<li> Additional variables for Ancestry:</li>
 +
<ul>
 
<div class="mw-collapsible" style="width:500px">
 
<div class="mw-collapsible" style="width:500px">
−
I'm using bash (replace the paths below with the appropriate paths):
+
<li>Using bash (replace the paths below with the appropriate paths):</li>
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
−
* Point to where you installed GotCloud
+
<pre>export REF=$SS/ancestry/ref&#10;export HGDP=$SS/ancestry/HGDP&#10;export BAM=$SS/ancestry/bams</pre>
−
*:<pre>export GC=/home/username/gotcloud</pre>
  −
* Point to where you installed the seqshop files
  −
*:<pre>export SS=/home/username/seqshop/</pre>
  −
* Point to where you want the output to go
  −
*:<pre>export OUT=/home/username/seqshop_output/</pre>
  −
* Additional variables for Ancestry:
  −
*:<pre>export REF=$SS/ancestry/ref&#10;export HGDP=$SS/ancestry/HGDP&#10;export BAM=$SS/ancestry/bams</pre>
   
</div>
 
</div>
 
</div>
 
</div>
−
   
<div class="mw-collapsible mw-collapsed" style="width:500px">
 
<div class="mw-collapsible mw-collapsed" style="width:500px">
−
I'm using tcsh (replace the paths below with the appropriate paths):
+
<li>Using tcsh (replace the paths below with the appropriate paths):</li>
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
−
* Point to where you installed GotCloud
+
<pre>setenv REF $SS/ancestry/ref&#10;setenv HGDP $SS/ancestry/HGDP&#10;setenv BAM $SS/ancestry/bams</pre>
−
*:<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>
  −
* Additional variables for Ancestry:
  −
*:<pre>setenv REF $SS/ancestry/ref&#10;setenv HGDP $SS/ancestry/HGDP&#10;setenv BAM $SS/ancestry/bams</pre>
   
</div>
 
</div>
 
</div>
 
</div>
−
 
+
</ul>
 +
</ul>
 
</div>
 
</div>
 
</div>
 
</div>
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/11184"

Navigation menu