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:

 biopipe-align_M.m_amd64.deb          aligner
 biopipe-umake_M.n_amd64.deb          umake
 biopipe-testalign_M.n_amd64.deb
 biopipe-testumake_M.n_amd64.deb

where 'M.n' are the normal major-minor version system. The package files are available from our public FTP site:

 #  The easiest way:
 mkdir debs
 cd debs
 wget ftp://share.sph.umich.edu/biopipe/\*.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 biopipe
 250 Directory successfully changed.
 ftp> mget biopipe*.deb
 ftp> quit
 221 Goodbye.

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/biopipe-align_*_amd64.deb
 Selecting previously unselected package biopipe-align.
 (Reading database ... 25372 files and directories currently installed.)
 Unpacking biopipe-align (from .../biopipe-align_M.n_amd64.deb) ...
 Setting up biopipe-align (M.n) ...
 Created symlink '/usr/local/bin/gen_biopipeline.pl' to make running the aligner easier.
 #============================================================
 #   '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'
 #============================================================
 #============================================================
 #   '/usr/local/biopipe/test/align' does not exist so you cannot test this install
 #   Install it by doing 'sudo dpkg -i biopipe-testalign*.deb'
 #============================================================

If there were messages about missing packages, install them now

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

Finally, install the other packages

 sudo dpkg -i debs/biopipe-umake_*_amd64.deb
 Selecting previously deselected package biopipe-umake.
 (Reading database ... 98799 files and directories currently installed.)
 Unpacking biopipe-umake (from .../biopipe-umake_M.n_amd64.deb) ...
 Setting up biopipe-umake (M.n) ...
 Created symlink '/usr/local/bin/umake.pl' to make running umake easier.
 Good, you appear to have 'make' installed
 Good, you appear to have 'libssl' installed at the correct level
 #============================================================
 #   '/usr/local/biopipe/test/umake' does not exist so you cannot test this install
 #   Install it by doing 'sudo dpkg -i biopipe-testumake_*.deb'
 #============================================================

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 signifcant changes to your Unix system.

 sudo dpkg -i debs/biopipe-test*_amd64.deb
 Unpacking biopipe-testalign (from .../biopipe-testalign_M.n_amd64.deb) ...
 Selecting previously deselected package biopipe-testumake.
 Unpacking biopipe-testumake (from .../biopipe-testumake_M.n_amd64.deb) ...
 Setting up biopipe-testalign (M.n) ...
 To test the pipeline, run:
 
   /usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign
 
 This will remove the contents of ~/testalign and then run
 the aligner test case. The output is verified so you know if
 anything failed or not.
 
 Setting up biopipe-testumake (M.n) ...
 To test umake, run:
 
   /usr/local/biopipe/bin/umake.pl --test ~/testumake
 
 This will remove the contents of ~/testumake and then run
 the umake test case. The output is verified so you know if
 anything failed or not.

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

 #   Test the aligner (fast, about 3 minutes)
 /usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign
 rm -rf ~/testalign              # If no error
 
 #   Test umake  (longer, about 15 minutes)
 /usr/local/biopipe/bin/umake.pl --test ~/testumake
 rm -rf ~/testumake              # If no error