Difference between revisions of "GotCloud: Binary Releases"
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Jump to navigationJump to searchTerry Gliedt (talk | contribs) |
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<code> | <code> | ||
| − | + | gotcloud-bin_M.m_amd64.deb aligner and umake | |
| − | + | gotcloud-test_M.n_amd64.deb test for software | |
| − | |||
| − | |||
</code> | </code> | ||
| Line 26: | Line 24: | ||
<b>mkdir debs</b> | <b>mkdir debs</b> | ||
<b>cd debs</b> | <b>cd debs</b> | ||
| − | <b>wget ftp://share.sph.umich.edu/ | + | <b>wget ftp://share.sph.umich.edu/gotcloud/gotcloud/\*.deb</b> |
# Another way: | # Another way: | ||
| Line 38: | Line 36: | ||
ftp> <b>prompt</b> | ftp> <b>prompt</b> | ||
Interactive mode off. | Interactive mode off. | ||
| − | ftp> <b>cd | + | ftp> <b>cd gotcloud</b> |
250 Directory successfully changed. | 250 Directory successfully changed. | ||
| − | ftp> <b>mget | + | ftp> <b>mget gotcloud*.deb</b> |
ftp> <b>quit</b> | ftp> <b>quit</b> | ||
221 Goodbye. | 221 Goodbye. | ||
| Line 52: | Line 50: | ||
<code> | <code> | ||
| − | <b>sudo dpkg -i debs/ | + | <b>sudo dpkg -i debs/gotcloud-bin_*_amd64.deb</b> |
| − | Selecting previously unselected package | + | Selecting previously unselected package gotcloud-bin. |
(Reading database ... 25372 files and directories currently installed.) | (Reading database ... 25372 files and directories currently installed.) | ||
| − | Unpacking | + | Unpacking gotcloud-bin (from .../gotcloud-bin_1.0_amd64.deb) ... |
| − | Setting up | + | Setting up gotcloud-bin (1.0) ... |
| − | |||
#============================================================ | #============================================================ | ||
# 'java' is not installed, do 'sudo apt-get install java-common default-jre' | # 'java' is not installed, do 'sudo apt-get install java-common default-jre' | ||
| Line 67: | Line 64: | ||
# 'libssl0.9.8' is not installed, do 'sudo apt-get install libssl0.9.8' | # 'libssl0.9.8' is not installed, do 'sudo apt-get install libssl0.9.8' | ||
#============================================================ | #============================================================ | ||
| − | + | ... | |
| − | |||
| − | |||
| − | |||
</code> | </code> | ||
| Line 76: | Line 70: | ||
<code> | <code> | ||
| − | <b>sudo apt-get install make libssl0.9.8 | + | <b>sudo apt-get update</b> |
| + | <b>sudo apt-get install java-common default-jre make libssl0.9.8</b> | ||
</code> | </code> | ||
| − | |||
| − | |||
| − | |||
| − | |||
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'''Testing the Installation''' | '''Testing the Installation''' | ||
| Line 102: | Line 81: | ||
The tests run within a few minutes and are self checking, so unless you see obvious errors, | 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 can be reasonably sure everything is set up properly. | ||
| − | You only need to do this once, unless you have made | + | You only need to do this once, unless you have made significant changes to your Unix system. |
<code> | <code> | ||
| − | <b>sudo dpkg -i debs/ | + | <b>sudo dpkg -i debs/gotcloud-test*_amd64.deb</b> |
| − | + | Selecting previously unselected package gotcloud-test. | |
| − | + | (Reading database ... 27376 files and directories currently installed.) | |
| − | Unpacking | + | Unpacking gotcloud-test (from .../gotcloud-test_1.0_amd64.deb) ... |
| − | Setting up | + | Setting up gotcloud-test (1.0) ... |
| − | To test the | + | #====================================================================== |
| + | # GotCloud README | ||
| + | #====================================================================== | ||
| + | To test the GotCloud aligner, run: | ||
| + | bin/gen_biopipeline.pl --test ~/testalign | ||
| + | This will create/clear the output directory ~/testalign. | ||
| + | Test results and a log file are put in this directory. | ||
| + | Results are self-checked and if errors should occur, it will be obvious. | ||
| − | + | To test the GotCloud umake, run: | |
| − | + | bin/umake.pl --test ~/testumake | |
| − | + | This will create/clear the output directory ~/testumake. | |
| − | + | Test results and a log file are put in this directory. | |
| − | + | Results are self-checked and if errors should occur, it will be obvious. | |
| − | + | ||
| − | |||
| − | To test umake, run: | ||
| − | |||
| − | |||
| − | |||
| − | This will | ||
| − | |||
| − | |||
</code> | </code> | ||
| − | Login as a normal user (not as root) and do: | + | Login as a normal user (ubuntu, not as root) and do: |
<code> | <code> | ||
| − | # Test the aligner ( | + | # Test the aligner (about 2 minutes) |
| − | <b>/usr/local/ | + | <b>/usr/local/gotcloud/bin/gen_biopipeline.pl --test ~/testalign</b> |
rm -rf ~/testalign # If no error | rm -rf ~/testalign # If no error | ||
| − | # Test umake ( | + | # Test umake (about 7 minutes) |
| − | <b>/usr/local/ | + | <b>/usr/local/gotcloud/bin/umake.pl --test ~/testumake</b> |
rm -rf ~/testumake # If no error | rm -rf ~/testumake # If no error | ||
</code> | </code> | ||
Revision as of 11:21, 10 December 2012
Installing Debian Packages
Back to parent: GotCloud
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:
gotcloud-bin_M.m_amd64.deb aligner and umake
gotcloud-test_M.n_amd64.deb test for software
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/gotcloud/gotcloud/\*.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 gotcloud
250 Directory successfully changed.
ftp> mget gotcloud*.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/gotcloud-bin_*_amd64.deb
Selecting previously unselected package gotcloud-bin.
(Reading database ... 25372 files and directories currently installed.)
Unpacking gotcloud-bin (from .../gotcloud-bin_1.0_amd64.deb) ...
Setting up gotcloud-bin (1.0) ...
#============================================================
# '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'
#============================================================
...
If there were messages about missing packages, install them now
sudo apt-get update
sudo apt-get install java-common default-jre make libssl0.9.8
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 significant changes to your Unix system.
sudo dpkg -i debs/gotcloud-test*_amd64.deb
Selecting previously unselected package gotcloud-test.
(Reading database ... 27376 files and directories currently installed.)
Unpacking gotcloud-test (from .../gotcloud-test_1.0_amd64.deb) ...
Setting up gotcloud-test (1.0) ...
#======================================================================
# GotCloud README
#======================================================================
To test the GotCloud aligner, run:
bin/gen_biopipeline.pl --test ~/testalign
This will create/clear the output directory ~/testalign.
Test results and a log file are put in this directory.
Results are self-checked and if errors should occur, it will be obvious.
To test the GotCloud umake, run:
bin/umake.pl --test ~/testumake
This will create/clear the output directory ~/testumake.
Test results and a log file are put in this directory.
Results are self-checked and if errors should occur, it will be obvious.
Login as a normal user (ubuntu, not as root) and do:
# Test the aligner (about 2 minutes)
/usr/local/gotcloud/bin/gen_biopipeline.pl --test ~/testalign
rm -rf ~/testalign # If no error
# Test umake (about 7 minutes)
/usr/local/gotcloud/bin/umake.pl --test ~/testumake
rm -rf ~/testumake # If no error
