Difference between revisions of "GotCloud: Binary Releases"

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−
'''Installing Debian Packages'''
+
Back to parent: [[GotCloud]]
 +
 
 +
 
 +
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.
 +
 
 +
 
 +
If you run into any problems with GotCloud, please check: [[GotCloud: FAQs]] or for problems/solutions for a specific version, [[GotCloud:_FAQs#Version_Problems|Version Problems]].
 +
 
 +
=GotCloud Binary Releases=
 +
GotCloud releases with the precompiled binary executables are available for download.
 +
 
 +
The binaries were compiled on Linux Ubuntu.
 +
 
 +
If you need the source, see [[GotCloud: Source Releases]] for information on obtaining the source.
 +
 
 +
The Binary Releases are available as:
 +
* [[#GotCloud_Debian_Packages|debian packages]] - require root access to install
 +
* [[#Tar Binary Releases|tarballs]] - anyone can untar
 +
 
 +
 
 +
The GotCloud software is distributed in several 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 a single package including both the ''aligner'' and ''variant caller''. 
  
−
Back to parent: [[GotCloud]]
+
There is also a separate package to test the installation.
  
 +
==GotCloud Debian Packages==
  
 +
If you would like to install from:
 +
* tar'd binary packages, see: [[#Tar Binary Releases|Tar Binary Releases]]
 +
* source (does not require root access), see: [[GotCloud: Source Releases]]
  
−
The GotCloud 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:
+
=== Installing Debian Packages ===
  
 +
The debian files are available for download from ftp://share.sph.umich.edu/gotcloud/ :
 
<code>
 
<code>
−
   gotcloud-bin_latest_amd64.deb          aligner and umake
+
   gotcloud-bin_latest_amd64.deb          aligner and variant caller
 
   gotcloud-test_latest_amd64.deb        test data for software
 
   gotcloud-test_latest_amd64.deb        test data for software
 +
  M.n/gotcloud-bin_M.n_amd64.deb        version M.n of aligner and variant caller
 +
  M.n/gotcloud-test_M.n_amd64.deb        version M.n of test data for software
 
</code>
 
</code>
 +
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.
  
−
where 'M.n' are the normal major-minor version system.
 
  
−
'''Fetch the Software Packages'''
+
====Fetch the GotCloud Debian Packages====
  
 
<code>
 
<code>
Line 22: Line 54:
 
   <b>mkdir debs</b>
 
   <b>mkdir debs</b>
 
   <b>cd debs</b>
 
   <b>cd debs</b>
−
   <b>wget ftp://share.sph.umich.edu/gotcloud/gotcloud\*latest\*.deb</b>
+
   <b>wget --retr-symlinks ftp://share.sph.umich.edu/gotcloud/gotcloud\*latest\*.deb</b>
 
   
 
   
 
   #  Another way:
 
   #  Another way:
Line 41: Line 73:
 
</code>
 
</code>
  
−
'''Install the Software'''
+
====Install the GotCloud Debian Packages====
  
−
Installation requires one to have <b>root access</b> and uses <b>dpkg</b> which Debian users will recognize.
+
<b>Install Debian packages with root access</b>
 +
 
 +
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:
Line 62: Line 96:
 
   #  '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 Installation'''
 
  
 
We recommend that at least the first time, you install the test packages so you can
 
We recommend that at least the first time, you install the test packages so you can
Line 91: Line 143:
 
   #======================================================================
 
   #======================================================================
 
   To test the GotCloud aligner, run:
 
   To test the GotCloud aligner, run:
−
     bin/gen_biopipeline.pl --test ~/testalign
+
     gotcloud align --test ~/testalign
 
   This will create/clear the output directory ~/testalign.
 
   This will create/clear the output directory ~/testalign.
 
   Test results and a log file are put in this directory.
 
   Test results and a log file are put in this directory.
 
   Results are self-checked and if errors should occur, it will be obvious.
 
   Results are self-checked and if errors should occur, it will be obvious.
 
    
 
    
−
   To test the GotCloud umake, run:
+
   To test the GotCloud snp caller, run:
−
     bin/umake.pl --test ~/testumake
+
     gotcloud snpcall --test ~/testsnp
−
   This will create/clear the output directory ~/testumake.
+
   This will create/clear the output directory ~/testsnp.
 
   Test results and a log file are put in this directory.
 
   Test results and a log file are put in this directory.
 
   Results are self-checked and if errors should occur, it will be obvious.
 
   Results are self-checked and if errors should occur, it will be obvious.
Line 104: Line 156:
 
</code>
 
</code>
  
−
Login as a normal user (ubuntu, not as root) and do:
+
Login as a normal user (not as root) and do:
  
 
<code>
 
<code>
−
   #  Test the aligner (2 minutes +/- 1 minute)
+
   #  Test the aligner (3 minutes +/- 1 minute)
−
   '''/usr/local/gotcloud/bin/gen_biopipeline.pl -test ~/testalign'''
+
   '''/usr/local/gotcloud/bin/gotcloud align -test ~/testalign'''
−
   Running GOTCLOUD TEST, test log in: /home/myuser/testalign/biopipeTest.log
+
  Removing any previous results from: /home/myuser/testalign/aligntest
−
   Created /home/myuser/testalign/biopipetest/Makefiles/biopipe_Sample2.Makefile
+
   Running GOTCLOUD TEST, test log in: /home/myuser/testalign/aligntest.log
−
   Created /home/myuser/testalign/biopipetest/Makefiles/biopipe_Sample1.Makefile
+
   Created /home/myuser/testalign/aligntest/Makefiles/align_Sample2.Makefile
 +
   Created /home/myuser/testalign/aligntest/Makefiles/align_Sample1.Makefile
 
   ---------------------------------------------------------------------
 
   ---------------------------------------------------------------------
−
  Submitted 2 local commands
+
   Waiting while samples are processed...
−
   Waiting for commands to complete... . .  Commands finished in 37 secs with no errors reported
+
  Processing finished in 63 secs with no errors reported
 
   Results from DIFF will be in /home/myuser/testalign/diff_logfiles_results.txt
 
   Results from DIFF will be in /home/myuser/testalign/diff_logfiles_results.txt
−
   Successful comparison of data in '/home/myuser/testalign' and '/usr/local/gotcloud/test/align/expected'
+
   Successful comparison of data in '/home/myuser/testalign/aligntest' and '/usr/local/gotcloud/test/align/expected/aligntest'
 
   Successfully ran the test case, congratulations!
 
   Successfully ran the test case, congratulations!
 
   '''rm -rf ~/testalign'''              # If no error
 
   '''rm -rf ~/testalign'''              # If no error
 
    
 
    
 
    
 
    
−
   #  Test umake (5 minutes +/-2 minute)
+
   #  Test snp calling (7 minutes +/-2 minute)
−
   '''/usr/local/gotcloud/bin/umake.pl --test ~/testumake'''
+
   '''/usr/local/gotcloud/bin/gotcloud snpcall --test ~/testsnp'''
−
   '''rm -rf ~/testumake'''              # If no error
+
  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 '/usr/local/gotcloud/test/umake/expected/umaketest'
 +
  Successfully ran the test case, congratulations!
 +
   '''rm -rf ~/testsnp'''              # If no error
 +
</code>
 +
 
 +
== Tar Binary Releases ==
 +
 
 +
The tar binary releases contain the precompiled binaries and scripts necessary to run gotcloud.
 +
 
 +
If you would like to install from:
 +
* debian packages, see: [[#GotCloud Debian Packages|Debian Packages]]
 +
* source, see: [[GotCloud: Source Releases]]
 +
 
 +
=== Installing Tar Releases ===
 +
 
 +
The tar files are available for download from ftp://share.sph.umich.edu/gotcloud/ :
 +
<code>
 +
  gotcloudBin_latest.tgz          aligner and variant caller
 +
  gotcloudTest_latest.tgz        test data for software
 +
  M.n/gotcloud-bin_M.n.tar.gz    version M.n of aligner and variant caller
 +
  M.n/gotcloud-test_M.n.tar.gz    version M.n of test data for software
 
</code>
 
</code>
 +
Where 'M.n' is replaced with the specific version numbers.
 +
 +
See [[GotCloud: Versions]] for details on the changes for each version.
  
−
'''Creating Your Own Debian Package From the Source'''
+
====Fetch the Tar Releases====
 +
 
 +
<code>
 +
  #  The easiest way:
 +
  <b>wget --retr-symlinks ftp://share.sph.umich.edu/gotcloud/gotcloud-\*latest\*.tgz</b>
 +
 +
  #  Another way:
 +
  <b>ftp share.sph.umich.edu</b>
 +
  Connected to share.sph.umich.edu.
 +
  220 (vsFTPd 2.3.5)
 +
  Name (share.sph.umich.edu:tpg): <b>anonymous</b>
 +
  230 Login successful.
 +
  Remote system type is UNIX.
 +
  Using binary mode to transfer files.
 +
  ftp> <b>prompt</b>
 +
  Interactive mode off.
 +
  ftp> <b>cd gotcloud</b>
 +
  250 Directory successfully changed.
 +
  ftp> <b>mget gotcloud-*latest*.tgz</b>
 +
  ftp> <b>quit</b>
 +
  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>
 +
 
 +
=Creating Your Own Debian Package From the Source=
  
 
The process to create your own Debian package from the source files is straight-forward
 
The process to create your own Debian package from the source files is straight-forward
 
for Debian users. The source files actually contain source for the executables,
 
for Debian users. The source files actually contain source for the executables,
 
the test data and the scripts and configuration files used by the users.
 
the test data and the scripts and configuration files used by the users.
−
To source builds two debian package files - one for the test data (test) and one for the
+
These steps build two debian package files - one for the test data (test) and one for the
 
binaries and scripts (bin).
 
binaries and scripts (bin).
  
−
In order to simply the build of two packages, the debian directory contains the control
+
In order to simplify the building of two packages, the debian directory contains the control files for both packages (bin and test).
−
files for both packages (bin and test).
 
 
This requires that the normal control files (e.g. rules) be named rules.test and rules.bin
 
This requires that the normal control files (e.g. rules) be named rules.test and rules.bin
 
and the shell script (makedeb.sh) be aware of this nuance.
 
and the shell script (makedeb.sh) be aware of this nuance.
Line 141: Line 283:
 
the version for GotCloud.
 
the version for GotCloud.
  
−
'''Fetch the Source'''
+
'''Fetch the Source Including the Test Files'''
  
 
<code>
 
<code>
 
  #  The easiest way:
 
  #  The easiest way:
−
  wget ftp://share.sph.umich.edu/gotcloud/gotcloud-src_latest.tgz
+
  wget ftp://share.sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz
  
 
  #  Another way:
 
  #  Another way:
Line 159: Line 301:
 
  ftp> cd gotcloud
 
  ftp> cd gotcloud
 
  250 Directory successfully changed.
 
  250 Directory successfully changed.
−
  ftp> get gotcloud-src_latest.tgz
+
  ftp> get gotcloudWithTest_latest.tgz
 
  ftp> quit
 
  ftp> quit
 
  221 Goodbye.
 
  221 Goodbye.
  
 
  #  Extract the source files
 
  #  Extract the source files
−
  cd ~/src                # Wherever you want the source files
+
  cd ~/src                # Or wherever you want the source files
−
  tar xzf path/gotcloud-src_latest.tgz
+
  tar xzf path/gotcloudWithTest_latest.tgz
 
</code>
 
</code>
  
−
'''Compile the Source'''
 
  
−
<code>
+
'''Fetch the Source Excluding the Test Files'''
−
cd ~/src
+
 
−
cd gotcloud*
+
Follow the above logic, but use: gotcloud_latest.tgz
−
cd src
+
 
−
cat INSTALL              # Read about dependencies
+
'''Fetch just the Test Files'''
−
make clean              # Clean out cruft from a previous run
+
 
−
make
+
Follow the above logic, but use: gotcloudTest_latest.tgz
−
</code>
+
 
  
−
'''Create the Debian Package Files'''
+
===Create the Debian Package Files===
  
 
<code>
 
<code>
−
  '''cd ~/src'''
+
  '''cd ~/src'''                 # Or wherever you put the source files
 
  '''cd gotcloud*'''
 
  '''cd gotcloud*'''
 +
 
  #  Add -replace only if rebuilding the same version
 
  #  Add -replace only if rebuilding the same version
−
  '''debian/makedeb.sh  bin  `cat release_version.txt`'''  
+
  '''debian/makedeb.sh  bin  ='''  
−
   dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security
+
   dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 ...
 
   dpkg-buildpackage: export C...
 
   dpkg-buildpackage: export C...
 
     [lines deleted]
 
     [lines deleted]
Line 199: Line 341:
 
     [lines deleted]
 
     [lines deleted]
 
   dpkg-deb: building package `gotcloud-bin' in `./gotcloud-bin_1.01_amd64.deb'.
 
   dpkg-deb: building package `gotcloud-bin' in `./gotcloud-bin_1.01_amd64.deb'.
−
   Package file now in /home/tpg/dev/gotcloud
+
   Package file now in /home/myuser/dev/gotcloud
−
   -rw-r--r-- 1 tpg tpg 3592780 Feb 19 11:59 gotcloud-bin_1.01_amd64.deb  
+
   -rw-r--r-- 1 myuser myuser 3592780 Feb 19 11:59 gotcloud-bin_1.01_amd64.deb
−
  '''debian/makedeb.sh  test `cat release_version.txt`'''
+
 +
#  Add -replace only if rebuilding the same version
 +
  '''debian/makedeb.sh  test ='''
 +
  dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 ...
 +
  dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): -D_FORTIFY_SOURCE=2
 +
    [lines deleted]
 +
  Generate package: cd gotcloud-test; dpkg-buildpackage -b -us -uc -rfakeroot
 +
  ===> Version '1.01 of 'gotcloud-test' will install into 'usr/local/gotcloud'
 +
  install -d debian/tmp/DEBIAN
 +
  cp debian/control debian/postinst debian/postrm debian/tmp/DEBIAN
 +
  install -d debian/tmp/usr/share/doc/gotcloud-test_1.01
 +
  sed -e s/99.99/1.01/g < debian/changelog > debian/changelog.new
 +
    [lines deleted]
 +
  dpkg-deb: building package `gotcloud-test' in `./gotcloud-test_1.01_amd64.deb'.
 +
  Package file now in /home/myuser/dev/gotcloud
 +
  -rw-r--r-- 1 myuser myuser 433269556 Feb 19 13:49 gotcloud-test_1.01_amd64.deb
 
</code>
 
</code>
  
 
The deb files will be created in the directory above the debian directory  (e.g. gotcloud)
 
The deb files will be created in the directory above the debian directory  (e.g. gotcloud)

Latest revision as of 23:29, 7 January 2016

Back to parent: GotCloud


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.


If you run into any problems with GotCloud, please check: GotCloud: FAQs or for problems/solutions for a specific version, Version Problems.

GotCloud Binary Releases

GotCloud releases with the precompiled binary executables are available for download.

The binaries were compiled on Linux Ubuntu.

If you need the source, see GotCloud: Source Releases for information on obtaining the source.

The Binary Releases are available as:


The GotCloud software is distributed in several 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 a single package including both the aligner and variant caller.

There is also a separate package to test the installation.

GotCloud Debian Packages

If you would like to install from:


Installing Debian Packages

The debian files are available for download from ftp://share.sph.umich.edu/gotcloud/ : 

 gotcloud-bin_latest_amd64.deb          aligner and variant caller
 gotcloud-test_latest_amd64.deb         test data for software
 M.n/gotcloud-bin_M.n_amd64.deb         version M.n of aligner and variant caller
 M.n/gotcloud-test_M.n_amd64.deb        version M.n of test data for software

Where 'M.n' is replaced with the specific version numbers.

Installing Debian packages normally requires root access, however, you can install as a non-root user (see below).

See GotCloud: Versions for details on the changes for each version.


Fetch the GotCloud Debian Packages

 #  The easiest way:
 mkdir debs
 cd debs
 wget --retr-symlinks ftp://share.sph.umich.edu/gotcloud/gotcloud\*latest\*.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*latest*.deb
 ftp> quit
 221 Goodbye.

Install the GotCloud Debian Packages

Install Debian packages with root access

Installation normally 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'
 #============================================================

 sudo dpkg -i ~/debs/gotcloud-test_*_amd64.deb

Install Debian packages without root access

Installing Debian packages generally requires root access, however, you can install as a non-root user using the following instructions (bash commands shown here): 

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

If there were messages about missing packages, install them with the commands shown by the script. Installing missing packages will require root access. 

 sudo apt-get update
 sudo apt-get install java-common default-jre make libssl0.9.8  # For example

Testing the GotCloud 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:
   gotcloud align --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 snp caller, run:
   gotcloud snpcall --test ~/testsnp
 This will create/clear the output directory ~/testsnp.
 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 (not as root) and do: 

 #   Test the aligner (3 minutes +/- 1 minute)
 /usr/local/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 '/usr/local/gotcloud/test/align/expected/aligntest'
 Successfully ran the test case, congratulations!
 rm -rf ~/testalign              # If no error
 
 
 #   Test snp calling  (7 minutes +/-2 minute)
 /usr/local/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 '/usr/local/gotcloud/test/umake/expected/umaketest'
 Successfully ran the test case, congratulations!
 rm -rf ~/testsnp              # If no error

Tar Binary Releases

The tar binary releases contain the precompiled binaries and scripts necessary to run gotcloud.

If you would like to install from:

Installing Tar Releases

The tar files are available for download from ftp://share.sph.umich.edu/gotcloud/ : 

 gotcloudBin_latest.tgz          aligner and variant caller
 gotcloudTest_latest.tgz         test data for software
 M.n/gotcloud-bin_M.n.tar.gz     version M.n of aligner and variant caller
 M.n/gotcloud-test_M.n.tar.gz    version M.n of test data for software

Where 'M.n' is replaced with the specific version numbers.

See GotCloud: Versions for details on the changes for each version.

Fetch the Tar Releases

 #  The easiest way:
 wget --retr-symlinks ftp://share.sph.umich.edu/gotcloud/gotcloud-\*latest\*.tgz

 #  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-*latest*.tgz
 ftp> quit
 221 Goodbye.

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. 

 #   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

Creating Your Own Debian Package From the Source

The process to create your own Debian package from the source files is straight-forward for Debian users. The source files actually contain source for the executables, the test data and the scripts and configuration files used by the users. These steps build two debian package files - one for the test data (test) and one for the binaries and scripts (bin).

In order to simplify the building of two packages, the debian directory contains the control files for both packages (bin and test). This requires that the normal control files (e.g. rules) be named rules.test and rules.bin and the shell script (makedeb.sh) be aware of this nuance. In addition the shell script can make an RPM file (using alien) and will help manage the version for GotCloud.

Fetch the Source Including the Test Files 

#  The easiest way:
wget ftp://share.sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz

#  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> get gotcloudWithTest_latest.tgz
ftp> quit
221 Goodbye.

#  Extract the source files
cd ~/src                 # Or wherever you want the source files
tar xzf path/gotcloudWithTest_latest.tgz


Fetch the Source Excluding the Test Files

Follow the above logic, but use: gotcloud_latest.tgz

Fetch just the Test Files

Follow the above logic, but use: gotcloudTest_latest.tgz


Create the Debian Package Files

cd ~/src                 # Or wherever you put the source files
cd gotcloud*

#   Add -replace only if rebuilding the same version
debian/makedeb.sh  bin  = 
 dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 ...
 dpkg-buildpackage: export C...
   [lines deleted]
 Generate package: cd gotcloud-bin; dpkg-buildpackage -b -us -uc -rfakeroot
 ===> Version '1.01 of 'gotcloud-bin' will install into 'usr/local/gotcloud'
 install -d debian/tmp/DEBIAN
 cp debian/control debian/postinst debian/postrm debian/tmp/DEBIAN
 install -d debian/tmp/usr/share/doc/gotcloud-bin_1.01
 sed -e s/99.99/1.01/g < debian/changelog > debian/changelog.new
   [lines deleted]
 Converting symlinks into the actual executables to be distributed
   [lines deleted]
 dpkg-deb: building package `gotcloud-bin' in `./gotcloud-bin_1.01_amd64.deb'.
 Package file now in /home/myuser/dev/gotcloud
 -rw-r--r-- 1 myuser myuser 3592780 Feb 19 11:59 gotcloud-bin_1.01_amd64.deb

#   Add -replace only if rebuilding the same version
debian/makedeb.sh  test =
 dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 ...
 dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): -D_FORTIFY_SOURCE=2
   [lines deleted]
 Generate package: cd gotcloud-test; dpkg-buildpackage -b -us -uc -rfakeroot
 ===> Version '1.01 of 'gotcloud-test' will install into 'usr/local/gotcloud'
 install -d debian/tmp/DEBIAN
 cp debian/control debian/postinst debian/postrm debian/tmp/DEBIAN
 install -d debian/tmp/usr/share/doc/gotcloud-test_1.01
 sed -e s/99.99/1.01/g < debian/changelog > debian/changelog.new
   [lines deleted]
 dpkg-deb: building package `gotcloud-test' in `./gotcloud-test_1.01_amd64.deb'.
 Package file now in /home/myuser/dev/gotcloud
 -rw-r--r-- 1 myuser myuser 433269556 Feb 19 13:49 gotcloud-test_1.01_amd64.deb

The deb files will be created in the directory above the debian directory (e.g. gotcloud)

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