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| The GotCloud software is distributed in several Debian packages. These can be installed on traditional Debian systems as well as Ubuntu (where it has been tested). The software should run on all versions from Ubuntu Lucid (9.04) through Oneric (12.10). It has not been tested on other Debian systems, but it is likely it will work on those systems too. This software should work on any Unix system - only requiring recompilation from the source files. | | The GotCloud software is distributed in several Debian packages. These can be installed on traditional Debian systems as well as Ubuntu (where it has been tested). The software should run on all versions from Ubuntu Lucid (9.04) through Oneric (12.10). It has not been tested on other Debian systems, but it is likely it will work on those systems too. This software should work on any Unix system - only requiring recompilation from the source files. |
| | | |
− | The software is distributed in two parts, the ''aligner'' and ''umake''. Each has a package to test the installation. The following naming conventions are used: | + | The software is distributed in a single package including both the ''aligner'' and ''variant caller''. THere is also a package to test the installation. The following naming conventions are used: |
| | | |
| <code> | | <code> |
− | gotcloud-bin_latest_amd64.deb aligner and umake | + | gotcloud-bin_M.n_amd64.deb aligner and variant caller |
− | gotcloud-test_latest_amd64.deb test data for software | + | gotcloud-test_M.n_amd64.deb test data for software |
| </code> | | </code> |
| | | |
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| #====================================================================== | | #====================================================================== |
| To test the GotCloud aligner, run: | | To test the GotCloud aligner, run: |
− | bin/gen_biopipeline.pl --test ~/testalign | + | gotcloud align --test ~/testalign |
| This will create/clear the output directory ~/testalign. | | This will create/clear the output directory ~/testalign. |
| Test results and a log file are put in this directory. | | Test results and a log file are put in this directory. |
| Results are self-checked and if errors should occur, it will be obvious. | | Results are self-checked and if errors should occur, it will be obvious. |
| | | |
− | To test the GotCloud umake, run: | + | To test the GotCloud snp caller, run: |
− | bin/umake.pl --test ~/testumake | + | gotcloud snpcall --test ~/testsnp |
− | This will create/clear the output directory ~/testumake. | + | This will create/clear the output directory ~/testsnp. |
| Test results and a log file are put in this directory. | | Test results and a log file are put in this directory. |
| Results are self-checked and if errors should occur, it will be obvious. | | Results are self-checked and if errors should occur, it will be obvious. |
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| <code> | | <code> |
| # Test the aligner (2 minutes +/- 1 minute) | | # Test the aligner (2 minutes +/- 1 minute) |
− | '''/usr/local/gotcloud/bin/gen_biopipeline.pl -test ~/testalign''' | + | '''/usr/local/gotcloud/bin/gotcloud align -test ~/testalign''' |
− | Running GOTCLOUD TEST, test log in: /home/myuser/testalign/biopipeTest.log | + | Removing any previous results from: /home/myuser/testalign/aligntest |
− | Created /home/myuser/testalign/biopipetest/Makefiles/biopipe_Sample2.Makefile | + | Running GOTCLOUD TEST, test log in: /home/myuser/testalign/aligntest.log |
− | Created /home/myuser/testalign/biopipetest/Makefiles/biopipe_Sample1.Makefile | + | Created /home/myuser/testalign/aligntest/Makefiles/align_Sample2.Makefile |
| + | Created /home/myuser/testalign/aligntest/Makefiles/align_Sample1.Makefile |
| --------------------------------------------------------------------- | | --------------------------------------------------------------------- |
− | Submitted 2 local commands
| + | Waiting while samples are processed... |
− | Waiting for commands to complete... . . Commands finished in 37 secs with no errors reported | + | Processing finished in 63 secs with no errors reported |
| Results from DIFF will be in /home/myuser/testalign/diff_logfiles_results.txt | | Results from DIFF will be in /home/myuser/testalign/diff_logfiles_results.txt |
− | Successful comparison of data in '/home/myuser/testalign' and '/usr/local/gotcloud/test/align/expected' | + | Successful comparison of data in '/home/myuser/testalign/aligntest' and '/usr/local/gotcloud/test/align/expected/aligntest' |
| Successfully ran the test case, congratulations! | | Successfully ran the test case, congratulations! |
| '''rm -rf ~/testalign''' # If no error | | '''rm -rf ~/testalign''' # If no error |
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| | | |
| # Test umake (5 minutes +/-2 minute) | | # Test umake (5 minutes +/-2 minute) |
− | '''/usr/local/gotcloud/bin/umake.pl --test ~/testumake''' | + | '''/usr/local/gotcloud/bin/gotcloud snpcall --test ~/testsnp''' |
− | '''rm -rf ~/testumake''' # If no error | + | 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 '/usr/local/gotcloud/test/umake/expected/umaketest' |
| + | Successfully ran the test case, congratulations! |
| + | '''rm -rf ~/testsnp''' # If no error |
| </code> | | </code> |
| | | |