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, 12:43, 29 January 2013
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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> |
− | # The easiest way:
| + | <b>cd /usr/local/gotcloud.ref</b> # Where you want the files installed |
− | <b>mkdir debs</b>
| + | <b>tar xzvf hs37-db132.tar.gz</b> |
− | <b>cd debs</b>
| + | <b>rm -f hs37-db132.tar.gz</b> |
− | <b>wget ftp://share.sph.umich.edu/gotcloud/gotcloud\*.deb</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. |