GotCloud: Binary Releases

Installing Debian Packages

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The BioPipeline 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:

 gotcloud-bin_M.m_amd64.deb          aligner and umake
 gotcloud-test_M.n_amd64.deb         test data for software

where 'M.n' are the normal major-minor version system.

Fetch the Software Packages

The package files are available from our public FTP site:

 #  The easiest way:
 mkdir debs
 cd debs
 wget ftp://share.sph.umich.edu/gotcloud/gotcloud\*.deb

 #  Another way:
 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 gotcloud*.deb
 ftp> quit
 221 Goodbye.

Install the Software

Installation requires one to have root access and uses dpkg which Debian users will recognize. We recommend you install the first one separately so you can easily identify messages about prerequisite files that need to be installed:

 sudo dpkg -i ~/debs/gotcloud-bin_*_amd64.deb
 Selecting previously unselected package gotcloud-bin.
 (Reading database ... 25372 files and directories currently installed.)
 Unpacking gotcloud-bin (from .../gotcloud-bin_1.0_amd64.deb) ...
 Setting up gotcloud-bin (1.0) ...
 #============================================================
 #   'java' is not installed, do 'sudo apt-get install java-common default-jre'
 #============================================================
 #============================================================
 #   'make' is not installed, do 'sudo apt-get install make'
 #============================================================
 #============================================================
 #   'libssl0.9.8' is not installed, do 'sudo apt-get install libssl0.9.8'
 #============================================================
 ...

If there were messages about missing packages, install them now

 sudo apt-get update
 sudo apt-get install java-common default-jre make libssl0.9.8

Testing the Installation

We recommend that at least the first time, you install 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.

 sudo dpkg -i ~/debs/gotcloud-test*_amd64.deb
 Selecting previously unselected package gotcloud-test.
 (Reading database ... 27376 files and directories currently installed.)
 Unpacking gotcloud-test (from .../gotcloud-test_1.0_amd64.deb) ...
 Setting up gotcloud-test (1.0) ...
 #======================================================================
 #   GotCloud README
 #======================================================================
 To test the GotCloud aligner, run:
   bin/gen_biopipeline.pl --test ~/testalign
 This will create/clear the output directory ~/testalign.
 Test results and a log file are put in this directory.
 Results are self-checked and if errors should occur, it will be obvious.
 
 To test the GotCloud umake, run:
   bin/umake.pl --test ~/testumake
 This will create/clear the output directory ~/testumake.
 Test results and a log file are put in this directory.
 Results are self-checked and if errors should occur, it will be obvious.

Login as a normal user (ubuntu, not as root) and do:

 #   Test the aligner (1-2 minutes)
 /usr/local/gotcloud/bin/gen_biopipeline.pl --test ~/testalign
 rm -rf ~/testalign              # If no error
 
 #   Test umake  (about 7 minutes)
 /usr/local/gotcloud/bin/umake.pl --test ~/testumake
 rm -rf ~/testumake              # If no error