Difference between revisions of "GotCloud: Genetic Reference and Resource Files"
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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> | ||
| + | # The easiest way to get the data: | ||
| + | <b>cd /tmp</b> | ||
| + | <b>wget ftp://share.sph.umich.edu/gotcloud/hs37-db132.tar.gz</b> | ||
| + | |||
| + | # Another way: | ||
| + | <b>cd /tmp</b> | ||
| + | <b>ftp share.sph.umich.edu</b> | ||
| + | Connected to share.sph.umich.edu. | ||
| + | 220 (vsFTPd 2.3.5) | ||
| + | Name (share.sph.umich.edu:tpg): anonymous | ||
| + | 230 Login successful. | ||
| + | Remote system type is UNIX. | ||
| + | Using binary mode to transfer files. | ||
| + | ftp> prompt | ||
| + | Interactive mode off. | ||
| + | ftp> cd gotcloud | ||
| + | 250 Directory successfully changed. | ||
| + | ftp> mget hs37-db132.tar.gz | ||
| + | ftp> quit | ||
| + | 221 Goodbye. | ||
| + | </code> | ||
| + | |||
| + | |||
| + | <b>cd /usr/local/gotcloud.ref</b> | ||
| + | <b>tar xzvf hs37-db132.tar.gz</b> | ||
| + | <b>rm -f hs37-db132.tar.gz</b> | ||
| + | |||
| + | Install the Files | ||
| + | |||
Choose a destination for these files and install them as shown below (we'll assume you will use '''/usr/local/gotcloud.ref'''). | Choose a destination for these files and install them as shown below (we'll assume you will use '''/usr/local/gotcloud.ref'''). | ||
<code> | <code> | ||
| − | + | <b>cd /usr/local/gotcloud.ref</b> # Where you want the files installed | |
| − | + | <b>tar xzvf hs37-db132.tar.gz</b> | |
| − | + | <b>rm -f hs37-db132.tar.gz</b> | |
| − | + | </code> | |
| + | |||
| + | Note this path as you will need to set the variable REF_DIR in the configuration file or options | ||
| + | gen_biopipeline.pl and umake. | ||
Revision as of 12:43, 29 January 2013
Installing Genetic Reference and Resource Files
Back to parent: GotCloud
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.
# The easiest way to get the data:
cd /tmp
wget ftp://share.sph.umich.edu/gotcloud/hs37-db132.tar.gz
# Another way:
cd /tmp
ftp share.sph.umich.edu
Connected to share.sph.umich.edu.
220 (vsFTPd 2.3.5)
Name (share.sph.umich.edu:tpg): anonymous
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> prompt
Interactive mode off.
ftp> cd gotcloud
250 Directory successfully changed.
ftp> mget hs37-db132.tar.gz
ftp> quit
221 Goodbye.
cd /usr/local/gotcloud.ref tar xzvf hs37-db132.tar.gz rm -f hs37-db132.tar.gz
Install the Files
Choose a destination for these files and install them as shown below (we'll assume you will use /usr/local/gotcloud.ref).
cd /usr/local/gotcloud.ref # Where you want the files installed
tar xzvf hs37-db132.tar.gz
rm -f hs37-db132.tar.gz
Note this path as you will need to set the variable REF_DIR in the configuration file or options gen_biopipeline.pl and umake.
