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