Changes

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>

   #======================================================================

   #======================================================================

   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.

<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

   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

   ---------------------------------------------------------------------

   ---------------------------------------------------------------------

   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

    

    

   #  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

   '''rm -rf ~/testsnp'''              # If no error

</code>

</code>