Difference between revisions of "GotCloud: Binary Releases"
Terry Gliedt (talk | contribs) |
Terry Gliedt (talk | contribs) |
||
Line 44: | Line 44: | ||
221 Goodbye. | 221 Goodbye. | ||
</code> | </code> | ||
− | ''' | + | |
− | Install the Software''' | + | '''Install the Software''' |
Installation requires one to have <b>root access</b> and uses <b>dpkg</b> which Debian users will recognize. | Installation requires one to have <b>root access</b> and uses <b>dpkg</b> which Debian users will recognize. |
Revision as of 13:29, 23 October 2012
Installing Debian Packages
Back to parent [1]
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.
Fetch the Software Packages
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.
Install the Software
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_M.n_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
sudo dpkg -i debs/biopipe-umake_*_amd64.deb
Selecting previously deselected package biopipe-umake.
(Reading database ... 98799 files and directories currently installed.)
Unpacking biopipe-umake (from .../biopipe-umake_M.n_amd64.deb) ...
Setting up biopipe-umake (M.n) ...
Created symlink '/usr/local/bin/umake.pl' to make running umake easier.
Good, you appear to have 'make' installed
Good, you appear to have 'libssl' installed at the correct level
#============================================================
# '/usr/local/biopipe/test/umake' does not exist so you cannot test this install
# Install it by doing 'sudo dpkg -i biopipe-testumake_*.deb'
#============================================================
Testing the Installation
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. You only need to do this once, unless you have made signifcant changes to your Unix system.
sudo dpkg -i debs/biopipe-test*_amd64.deb
Unpacking biopipe-testalign (from .../biopipe-testalign_M.n_amd64.deb) ...
Selecting previously deselected package biopipe-testumake.
Unpacking biopipe-testumake (from .../biopipe-testumake_M.n_amd64.deb) ...
Setting up biopipe-testalign (M.n) ...
To test the pipeline, run:
/usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign
This will remove the contents of ~/testalign and then run
the aligner test case. The output is verified so you know if
anything failed or not.
Setting up biopipe-testumake (M.n) ...
To test umake, run:
/usr/local/biopipe/bin/umake.pl --test ~/testumake
This will remove the contents of ~/testumake and then run
the umake test case. The output is verified so you know if
anything failed or not.
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