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-testumake_M.n_amd64.deb      test cases for each
 biopipe-testalign_M.n_amd64.deb

The package files are available from our public FTP site:

Installation requires one to have root access and uses dpkg Ubuntu users will recognize:

ssh -i ~/.ssh/AWS/CSG.pem ubuntu@ec2-23-20-32-7.compute-1.amazonaws.com

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.

1. ============================================================
2. 'java' is not installed, do 'sudo apt-get install java-common default-jre'
3. ============================================================
4. ============================================================
5. 'make' is not installed, do 'sudo apt-get install make'
6. ============================================================
7. ============================================================
8. 'libssl0.9.8' is not installed, do 'sudo apt-get install libssl0.9.8'
9. ============================================================
10. ============================================================
11. '/usr/local/biopipe/test/align' does not exist so you cannot test this install
12. Install it by doing 'sudo dpkg -i biopipe-test_*.deb'
13. ============================================================

etc

If there were messages about missing packages, install them now

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

sudo dpkg -i debs/biopipe-testalign_0.6_amd64.deb

/usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign