Difference between revisions of "GotCloud: Binary Releases"
Terry Gliedt (talk | contribs) |
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# The easiest way: | # The easiest way: | ||
+ | <b>mkdir debs</b> | ||
+ | <b>cd debs</b> | ||
<b>wget ftp://share.sph.umich.edu/biopipe/\*.deb</b> | <b>wget ftp://share.sph.umich.edu/biopipe/\*.deb</b> | ||
Revision as of 13:02, 23 October 2012
Installing Debian Packages
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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 it 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-testalign_M.n_amd64.deb
biopipe-testumake_M.n_amd64.deb
where 'M.n' are the normal major-minor version system. The package files are available from our public FTP site:
# The easiest way:
mkdir debs
cd debs
wget ftp://share.sph.umich.edu/biopipe/\*.deb
# 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*.deb
ftp> quit
221 Goodbye.
Installation requires one to have root access and uses dpkg which Debian 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 dpkg -i debs/biopipe-align_*_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 (M.n) ...
Created symlink '/usr/local/bin/gen_biopipeline.pl' to make running the aligner easier.
#============================================================
# 'java' is not installed, do 'sudo apt-get install java-common default-jre'
#============================================================
#============================================================
# 'make' is not installed, do 'sudo apt-get install make'
#============================================================
#============================================================
# 'libssl0.9.8' is not installed, do 'sudo apt-get install libssl0.9.8'
#============================================================
#============================================================
# '/usr/local/biopipe/test/align' does not exist so you cannot test this install
# Install it by doing 'sudo dpkg -i biopipe-testalign*.deb'
#============================================================
If there were messages about missing packages, install them now
sudo apt-get install make libssl0.9.8 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 dpkg -i biopipe-umake_*_amd64.deb
sudo dpkg -i biopipe-test*_amd64.deb
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