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Revision as of 23:29, 7 January 2016
, 23:29, 7 January 2016no edit summary
The [[GotCloud]] software has been developed and tested on Linux Ubuntu 12.10 and 12.04.2 LTS. While it should work on other Linux systems, they have not yet been tested. It is not supported on Windows.
The [[GotCloud]] software has been developed and tested on Ubuntu Linux 12.04 and newer and Red Hat Enterprise Linux 6. While it should work on other Linux systems, they have not yet been tested. It is not supported on Windows or Mac OS X.
The Binary Releases are available as:
The Binary Releases are available as:
* [[#Debian Packages|debian packages]] - require root access to install
* [[#GotCloud_Debian_Packages|debian packages]] - require root access to install
* [[#Tar Binary Releases|tarballs]] - anyone can untar
* [[#Tar Binary Releases|tarballs]] - anyone can untar
==GotCloud Debian Packages==
==GotCloud Debian Packages==
If you would like to install from:
If you would like to install from:
</code>
</code>
Where 'M.n' is replaced with the specific version numbers.
Where 'M.n' is replaced with the specific version numbers.
Installing Debian packages normally requires root access, however, you <b>can</b> install as a non-root user (see below).
See [[GotCloud: Versions]] for details on the changes for each version.
See [[GotCloud: Versions]] for details on the changes for each version.
</code>
</code>
====Install the GotCloud Debian bin Package====
====Install the GotCloud Debian Packages====
<b>Install Debian packages with root access</b>
Installation requires one to have <b>root access</b> and uses <b>dpkg</b> which Debian users will recognize.
Installation normally requires one to have <b>root access</b> and uses <b>dpkg</b> which Debian users will recognize.
We recommend you install the first one separately so you can easily
We recommend you install the first one separately so you can easily
identify messages about prerequisite files that need to be installed:
identify messages about prerequisite files that need to be installed:
# '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'
#============================================================
#============================================================
...
<b>sudo dpkg -i ~/debs/gotcloud-test_*_amd64.deb</b>
</code>
<b>Install Debian packages without root access</b>
Installing Debian packages generally requires root access, however, you can install as a non-root user using the following instructions (bash commands shown here):
<code>
tempdir=/tmp/$$.gotcloud.removeme # Temp directory
destdir=$HOME # Where you want GotCloud installed
dpkg -x [path_to_deb_file]/gotcloud-bin_*_amd64.deb $tempdir
rsync -av --delete $tempdir/usr/local/gotcloud/* $destdir/gotcloud || exit 1
rm -rf $tempdir
dpkg -x [path_to_deb_file]/gotcloud-test_*_amd64.deb $tempdir
rsync -av --delete $tempdir/usr/local/gotcloud/* $destdir/gotcloud || exit 1
rm -rf $tempdir
$destdir/gotcloud/scripts/check_requirements.sh # Check requirements
</code>
</code>
If there were messages about missing packages, install them now
If there were messages about missing packages, install them with the commands shown by the script. Installing missing packages <b>will</b> require root access.
<code>
<code>
<b>sudo apt-get update</b>
<b>sudo apt-get update</b>
<b>sudo apt-get install java-common default-jre make libssl0.9.8</b>
<b>sudo apt-get install java-common default-jre make libssl0.9.8</b> # For example
</code>
</code>
===Testing the GotCloud Installation===
===Testing the GotCloud Installation===
'''rm -rf ~/testsnp''' # If no error
'''rm -rf ~/testsnp''' # If no error
</code>
</code>
== Tar Binary Releases ==
== Tar Binary Releases ==
See [[GotCloud: Versions]] for details on the changes for each version.
See [[GotCloud: Versions]] for details on the changes for each version.
====Fetch the Tar Releases====
====Fetch the Tar Releases====
<code>
<code>
# The easiest way:
# The easiest way:
<b>wget --retr-symlinks ftp://share.sph.umich.edu/gotcloud/gotcloud-\*latest\*.tgz</b>
<b>wget --retr-symlinks ftp://share.sph.umich.edu/gotcloud/gotcloud\*latest\*.tgz</b>
# Another way:
# Another way:
ftp> <b>cd gotcloud</b>
ftp> <b>cd gotcloud</b>
250 Directory successfully changed.
250 Directory successfully changed.
ftp> <b>mget gotcloud*latest*.tgz</b>
ftp> <b>mget gotcloud-*latest*.tgz</b>
ftp> <b>quit</b>
ftp> <b>quit</b>
221 Goodbye.
221 Goodbye.
</code>
====Unpack the Tar Release====
Unpack the realeases:
tar xf gotcloud-*latest*.tgz
===Testing the GotCloud Release===
We recommend that at least the first time, you download 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.
The test case results are self-checked and if errors should occur, it will be obvious.
<code>
# Test the aligner (3 minutes +/- 1 minute)
'''gotcloud/bin/gotcloud align --test ~/testalign'''
Removing any previous results from: /home/myuser/testalign/aligntest
Running GOTCLOUD TEST, test log in: /home/myuser/testalign/aligntest.log
Created /home/myuser/testalign/aligntest/Makefiles/align_Sample2.Makefile
Created /home/myuser/testalign/aligntest/Makefiles/align_Sample1.Makefile
---------------------------------------------------------------------
Waiting while samples are processed...
Processing finished in 63 secs with no errors reported
Results from DIFF will be in /home/myuser/testalign/diff_logfiles_results.txt
Successful comparison of data in '/home/myuser/testalign/aligntest' and 'gotcloud/test/align/expected/aligntest'
Successfully ran the test case, congratulations!
'''rm -rf ~/testalign''' # If no error
# Test snp calling (7 minutes +/-2 minute)
'''gotcloud/bin/gotcloud snpcall --test ~/testsnp'''
Removing any previous results from: /home/myuser/testsnp/umaketest
Running GOTCLOUD TEST, test log in: /home/myuser/testsnp/umaketest.log
Results from DIFF will be in /home/myuser/testsnp/diff_logfiles_results_umake.txt
Successful comparison of data in '/home/myuser/testsnp/umaketest' and 'gotcloud/test/umake/expected/umaketest'
Successfully ran the test case, congratulations!
'''rm -rf ~/testsnp''' # If no error
</code>
</code>
