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− | 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.
| + | '''Installing RPM Packages''' |
| + | |
| + | Back to parent [http://genome.sph.umich.edu/wiki/Pipelines] |
| + | |
| + | '''Note - RPMs are not generated at this time''' |
| + | |
| + | |
| + | The BioPipeline 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> |