Changes

'''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.

Choose a destination for these files and install them as shown below.  We'll assume you will use '''gotcloud/gotcloud.ref'''.  Replace <code>gotcloud</code> with the path to where you installed gotcloud.

<code>

<code>

  <b>mkdir -p /usr/local/gotcloud.ref</b>   # Where you want the files installed

  <b>cd /usr/local/gotcloud.ref</b>

  <b>mkdir -p gotcloud.ref</b>

  <b>cd gotcloud.ref</b>

</code>

</code>

Note this path as you will need to set the variable '''REF_DIR''' in the configuration file for gotcloud.

If you use a path other than a gotcloud.ref subdirectory of gotcloud, note this path as you will need to set the variable '''REF_DIR''' in the configuration file to point to the installation path.

'''Get the Resource Files'''

'''Get the Resource Files'''

The GotCloud Aligner and Umake makes use of various reference and other genetic resource files.

GotCloud 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.