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Revision as of 16:20, 22 October 2012
, 16:20, 22 October 2012no edit summary
biopipe-align_M.m_amd64.deb Aligner
biopipe-align_M.m_amd64.deb Aligner
biopipe-umake_M.n_amd64.deb umake
biopipe-umake_M.n_amd64.deb umake
biopipe-testalign_M.n_amd64.deb
biopipe-testalign_M.n_amd64.deb
biopipe-testumake_M.n_amd64.deb
</code>
</code>
The package files are available from our public FTP site:
The package files are available from our public FTP site:
<code>
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> cd biopipe
250 Directory successfully changed.
ftp> mget biopip*.deb
ftp> quit
221 Goodbye.
</code>
Installation requires one to have root access and uses dpkg Ubuntu users will recognize. We recommend you install the first one separately so it can identify prerequisite files:
<code>
sudo dpkg -i debs/biopipe-align_0.6_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 (0.6) ...
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-test_*.deb'
#============================================================
</code>
If there were messages about missing packages, install them now
<code>
<code>
sudo apt-get install make libssl0.9.8 java-common default-jre
sudo apt-get install make libssl0.9.8 java-common default-jre
</code>
sudo dpkg -i debs/biopipe-testalign_0.6_amd64.deb
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>
sudo dpkg -i biopipe-testalign_0.6_amd64.deb biopipe-umake_M.n_amd64.deb biopipe-testumake_M.n_amd64.deb
<code>
/usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign
/usr/local/biopipe/bin/gen_biopipeline.pl --test ~/testalign
</code>
</code>
