GotCloud: RedHat Package

Installing RPM Packages

Back to parent: GotCloud

Note - RPMs are not generated at this time

The GotCloud software is distributed in several RPM packages. These can be installed on Fedora, CentOS or Redhat systems. It has only been tested on CentOS 6.3, but should run on any recent Redhat-based system. 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.x86_64.rpm          aligner
 biopipe-umake_M.n.x86_64.rpm          umake
 biopipe-testalign_M.n.x86_64.rpm
 biopipe-testumake_M.n.x86_64.rpm

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

 #  The easiest way:
 wget ftp://share.sph.umich.edu/biopipe/\*.rpm

 #  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*.rpm
 ftp> quit
 221 Goodbye.

Installation requires one to have root access and uses rpm which Redhat 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 rpm -i debs/biopipe-align_*.rpm
 
   details to come here
 
 Created symlink '/usr/local/bin/gen_biopipeline.pl' to make running the aligner easier.
 #============================================================
 #   'java' is not installed, do 'sudo yum install java ???'
 #============================================================
 #============================================================
 #   'make' is not installed, do 'sudo yum install make'
 #============================================================
 #============================================================
 #   '/usr/local/biopipe/test/align' does not exist so you cannot test this install
 #   Install it by doing 'sudo rpm -i biopipe-testalign*.rpm'
 #============================================================

If there were messages about missing packages, install them now

 sudo yum install make 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 rpm -i biopipe-umake_*.rpm
 
 sudo rpm -i biopipe-test*.rpm

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
 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