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Line 29: Line 29:  
  #  The easiest way to get the data:
 
  #  The easiest way to get the data:
 
  <b>cd /tmp</b>
 
  <b>cd /tmp</b>
  <b>wget ftp://share.sph.umich.edu/gotcloud/hs37-db132.tar.gz</b>
+
  <b>wget ftp://share.sph.umich.edu/gotcloud/h37-db135.tgz</b>
    
  #  Another way:
 
  #  Another way:
Line 44: Line 44:  
  ftp> <b>cd gotcloud</b>
 
  ftp> <b>cd gotcloud</b>
 
  250 Directory successfully changed.
 
  250 Directory successfully changed.
  ftp> <b>mget hs37-db132.tar.gz</b>
+
  ftp> <b>mget h37-db135.tar.gz</b>
 
  ftp> <b>quit</b>
 
  ftp> <b>quit</b>
 
  221 Goodbye.
 
  221 Goodbye.
Line 56: Line 56:  
  <b>mkdir -p /usr/local/gotcloud.ref</b>    # Where you want the files installed
 
  <b>mkdir -p /usr/local/gotcloud.ref</b>    # Where you want the files installed
 
  <b>cd /usr/local/gotcloud.ref</b>
 
  <b>cd /usr/local/gotcloud.ref</b>
  <b>tar xzvf hs37-db132.tar.gz</b>
+
  <b>tar xzf h37-db135.tar.gz</b>
  ref/
+
  <b>rm -f h37-db135.tar.gz</b>
  ref/hs37d5.fa.fai
  −
  ref/metabochip.batch2.broken.b37.chr2.plink.MAF01.bed
  −
  ref/hs37d5-bs.umfa
  −
  ref/metabochip.batch2.broken.b37.chr2.plink.MAF01.fam
  −
  ref/dbsnp_132.b37.vcf.gz.tbi
  −
  ref/dbsnp_132.UCSC.coordinates.tbl
  −
    [lines deleted]
  −
  <b>rm -f hs37-db132.tar.gz</b>
   
</code>
 
</code>
   −
Note this path as you will need to set the variable '''REF_DIR''' in the configuration file or options
+
Note this path as you will need to set the variable '''REF_DIR''' in the configuration file for gotcloud.
'''gen_biopipeline.pl''' and '''umake.pl'''.
  −
 
      
= Using Your own Reference Files =
 
= Using Your own Reference Files =

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