GotCloud: Binary Releases

Debian Packages

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 they 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

The package files are available from our public FTP site:

 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> cd biopipe
 250 Directory successfully changed.
 ftp> mget biopip*.deb
 ftp> quit
 221 Goodbye.

Installation requires one to have root access and uses dpkg Ubuntu users will recognize. We recommend you install the first one separately so it can identify prerequisite files:

 sudo dpkg -i debs/biopipe-align_0.6_amd64.deb
 Selecting previously unselected package biopipe-align.
 (Reading database ... 25372 files and directories currently installed.)
 Unpacking biopipe-align (from .../biopipe-align_0.6_amd64.deb) ...
 Setting up biopipe-align (0.6) ...
 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-test_*.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. 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.

 sudo dpkg -i biopipe-umake_M.n_amd64.deb
 sudo dpkg -i biopipe-testalign_0.6_amd64.deb biopipe-testumake_M.n_amd64.deb

If you installed the test packages, test your installation. You only need to do this once, unless you have made signifcant changes to your Unix system. 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

 #   Test umake  (longer, about 15 minutes)
 /usr/local/biopipe/bin/umake.pl --test ~/testumake