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Line 1: − For the moment, we are not creating Redhat (Fedora) RPM packages. When we do, they will behave exactly like the Debian packages and their names will be nearly identical.+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
moved Pipeline RedHatPackage to GotCloud: RedHat Package
'''Installing RPM Packages'''
Back to parent: [[GotCloud]]
'''<font color='red'>Note - RPMs are not generated at this time</font>'''
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:
<code>
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
</code>
where 'M.n' are the normal major-minor version system.
The package files are available from our public FTP site:
<code>
# The easiest way:
<b>wget ftp://share.sph.umich.edu/biopipe/\*.rpm</b>
# Another way
<b>ftp share.sph.umich.edu</b>
Connected to share.sph.umich.edu.
220 (vsFTPd 2.3.5)
Name (share.sph.umich.edu:tpg): <b>anonymous</b>
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> <b>prompt</b>
Interactive mode off.
ftp> <b>cd biopipe</b>
250 Directory successfully changed.
ftp> <b>mget biopipe*.rpm</b>
ftp> <b>quit</b>
221 Goodbye.
</code>
Installation requires one to have <b>root access</b> and uses <b>rpm</b> 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:
<code>
<b>sudo rpm -i debs/biopipe-align_*.rpm</b>
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'
#============================================================
</code>
If there were messages about missing packages, install them now
<code>
<b>sudo yum install make java-common default-jre ????</b>
</code>
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.
<code>
<b>sudo rpm -i biopipe-umake_*.rpm</b>
<b>sudo rpm -i biopipe-test*.rpm</b>
</code>
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:
<code>
# Test the aligner (fast, about 3 minutes)
<b>/usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign</b>
rm -rf ~/testalign # If no error
# Test umake (longer, about 15 minutes)
<b>/usr/local/biopipe/bin/umake.pl --test ~/testumake</b>
rm -rf ~/testumake # If no error
</code>
