Line 191: |
Line 191: |
| <code> | | <code> |
| # The easiest way: | | # The easiest way: |
− | <b>wget --retr-symlinks ftp://share.sph.umich.edu/gotcloud/gotcloud\*latest\*.tgz</b> | + | <b>wget --retr-symlinks ftp://share.sph.umich.edu/gotcloud/gotcloud-\*latest\*.tgz</b> |
| | | |
| # Another way: | | # Another way: |
Line 205: |
Line 205: |
| ftp> <b>cd gotcloud</b> | | ftp> <b>cd gotcloud</b> |
| 250 Directory successfully changed. | | 250 Directory successfully changed. |
− | ftp> <b>mget gotcloud*latest*.tgz</b> | + | ftp> <b>mget gotcloud-*latest*.tgz</b> |
| ftp> <b>quit</b> | | ftp> <b>quit</b> |
| 221 Goodbye. | | 221 Goodbye. |
| + | </code> |
| + | |
| + | ====Unpack the Tar Release==== |
| + | |
| + | Unpack the realeases: |
| + | tar xf gotcloud-*latest*.tgz |
| + | |
| + | |
| + | |
| + | |
| + | ===Testing the GotCloud Installation=== |
| + | |
| + | We recommend that at least the first time, you download the test packages so you can |
| + | conveniently test the installation and make sure everything runs smoothly. |
| + | The tests run within a few minutes and are self checking, so unless you see obvious errors, |
| + | you can be reasonably sure everything is set up properly. |
| + | You only need to do this once, unless you have made significant changes to your Unix system. |
| + | |
| + | The test case results are self-checked and if errors should occur, it will be obvious. |
| + | |
| + | <code> |
| + | # Test the aligner (3 minutes +/- 1 minute) |
| + | '''gotcloud/bin/gotcloud align --test ~/testalign''' |
| + | Removing any previous results from: /home/myuser/testalign/aligntest |
| + | Running GOTCLOUD TEST, test log in: /home/myuser/testalign/aligntest.log |
| + | Created /home/myuser/testalign/aligntest/Makefiles/align_Sample2.Makefile |
| + | Created /home/myuser/testalign/aligntest/Makefiles/align_Sample1.Makefile |
| + | --------------------------------------------------------------------- |
| + | Waiting while samples are processed... |
| + | Processing finished in 63 secs with no errors reported |
| + | Results from DIFF will be in /home/myuser/testalign/diff_logfiles_results.txt |
| + | Successful comparison of data in '/home/myuser/testalign/aligntest' and 'gotcloud/test/align/expected/aligntest' |
| + | Successfully ran the test case, congratulations! |
| + | '''rm -rf ~/testalign''' # If no error |
| + | |
| + | |
| + | # Test snp calling (7 minutes +/-2 minute) |
| + | '''gotcloud/bin/gotcloud snpcall --test ~/testsnp''' |
| + | Removing any previous results from: /home/myuser/testsnp/umaketest |
| + | Running GOTCLOUD TEST, test log in: /home/myuser/testsnp/umaketest.log |
| + | Results from DIFF will be in /home/myuser/testsnp/diff_logfiles_results_umake.txt |
| + | Successful comparison of data in '/home/myuser/testsnp/umaketest' and 'gotcloud/test/umake/expected/umaketest' |
| + | Successfully ran the test case, congratulations! |
| + | '''rm -rf ~/testsnp''' # If no error |
| </code> | | </code> |
| | | |