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Revision as of 11:26, 27 January 2014
, 11:26, 27 January 2014no edit summary
'''Installing Genetic Reference and Resource Files'''
'''Installing Genetic Reference and Resource Files'''
Choose a destination for these files and install them as shown below. We'll assume you will use '''/usr/local/gotcloud.ref'''. If you use a different directory, replace /usr/local/gotcloud.ref with your path.
<code>
<b>mkdir -p /usr/local/gotcloud.ref</b> # Where you want the files installed
<b>cd /usr/local/gotcloud.ref</b>
</code>
Note this path as you will need to set the variable '''REF_DIR''' in the configuration file for gotcloud.
'''Get the Resource Files
'''Get the Resource Files'''
'''
The GotCloud Aligner and Umake makes use of various reference and other genetic resource files.
The GotCloud Aligner and Umake makes use of various reference and other genetic resource files.
You are free to use your own files, of course, but we also are making the files we use available.
You are free to use your own files, of course, but we also are making the files we use available.
<code>
<code>
# The easiest way to get the data:
# The easiest way to get the data:
<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db135-v2.tgz</b>
<b>wget ftp://anonymous@share.sph.umich.edu/gotcloud/ref/h37-db135-v2.tgz</b>
# Another way:
# Another way:
<b>ftp share.sph.umich.edu</b>
<b>ftp share.sph.umich.edu</b>
Connected to share.sph.umich.edu.
Connected to share.sph.umich.edu.
'''Install the Resource Files'''
'''Install the Resource Files'''
<code>
<code>
<b>tar xzf h37-db135-v2.tgz</b>
<b>tar xzf h37-db135-v2.tgz</b>
<b>rm -f h37-db135-v2.tgz</b>
<b>rm -f h37-db135-v2.tgz</b>
</code>
</code>
= Using Your own Reference Files =
= Using Your own Reference Files =
