Difference between revisions of "GotCloud: Source Releases"

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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]].
 
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]].
  
−
Tar versions of gotcloud can be downloaded from github.
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= Where to Find It =
  
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You can download either a specific release, the latest release, or the current development version.
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{{ToolGitRepo|repoName=gotcloud|nolibStatGen=true|noDownload=true|latestReleaseBranch=latest|skipBuild=true}}
  
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===Downloading a specific release===
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== Releases ==
 +
Released Versions are documented at [[GotCloud: Versions]] with details on the changes for each version.
  
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See https://github.com/statgen/gotcloud/releases for the list of specific releases that can be downloaded.
 
  
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You can download by:
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= Building =
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* Selecting the <code>zip</code> or <code>tar.gz</code> button near the version.
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Prior to running gotcloud, you need to compile the source.
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* Using wget to pull it directly:
 
  
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===Downloading the latest release===
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# cd into the gotcloud directory you just created (via clone/unzip/untar)
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We track the latest release using a branch called <code>latest</code>.
 
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The commandline for downloading this branch is:
 
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=== Downloading the current development version===
 
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If you are using the current development, I'd recommend using git.
 
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== Previous GotCloud Versions ==
 
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You can access previous gotcloud versions using the git tags by either directly downloading the previous version or by using git to set the view to a specific tag.
 
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See [[GotCloud: Versions]] for details on the changes for each version.
 
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== Downloading & Building GotCloud ==
 
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Here are the steps for installing from the source tar:
 
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# Create & change to the directory where you want gotcloud installed
 
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#: <pre>cd ~    # Replace ~ with the location where you want gotcloud installed.</pre>
 
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# Download the gotcloud tar from the ftp site.
 
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#: <pre>wget ftp://share.sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz</pre>
 
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# Extract the tar (In this example, it is the tar with the test files)
 
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#: <pre>tar xzf gotcloud_latest.tgz</pre>
 
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#* This will create a gotcloud directory containing the contents of the tar.
 
 
# Build (compile) the source
 
# Build (compile) the source
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#: <pre>cd gotcloud/src; make; cd ..</pre>
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#: <pre>cd src; make; cd ..</pre>
 
#* Note: as the source builds, many messages will scroll through your terminal.  You may even see some warnings.  These messages are normal and expected.  As long as the build does not end with an error, you have successfully built the source.
 
#* Note: as the source builds, many messages will scroll through your terminal.  You may even see some warnings.  These messages are normal and expected.  As long as the build does not end with an error, you have successfully built the source.
  
−
+
= GotCloud Script =
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GotCloud requires the following tools to be installed. 
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The gotcloud script that is the gateway to running GotCloud is found in the directory you created via clone/unzip/untar and is called gotcloud.
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* java (java-common default-jre on ubuntu)
 
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* make (make on ubuntu)
 
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* libssl (libssl0.9.8 on ubuntu)
 
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* gcc 4.4 or newer
 
  
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To check these requirements, run:
+
If you cloned into your home directory, it would be:
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  scripts/check_requirements.sh .
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  ~/gotcloud/gotcloud
 +
If you downloaded "latest" into your home directory, it would be:
 +
~/gotcloud-latest/gotcloud
  
−
 
−
The gotcloud script that is the gateway to running GotCloud is found in the path where you untarred the program under the gotcloud directory and is called gotcloud:
 
−
gotcloud/gotcloud
 
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If you downloaded and untarred into your home directory, it would be:
 
−
~/gotcloud/gotcloud
 
  
 
== Testing GotCloud ==
 
== Testing GotCloud ==
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If you installed the test files, you can run an automated test that will tell you if it passes or fails.
+
You can run an automated test that will tell you if it passes or fails.
  
−
This test will ensure that everything is setup/installed properly and produces the expected results.
+
This test will ensure that everything is setup/installed properly and the expected results are produced.
  
 
=== Test the aligner ===
 
=== Test the aligner ===
Line 92: Line 57:
 
  Successfully ran the test case, congratulations!
 
  Successfully ran the test case, congratulations!
  
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You can then remove the output directory if there were no errors.
+
You can remove the output directory if there were no errors.
 
  rm -rf ~/testalign
 
  rm -rf ~/testalign
  
Line 111: Line 76:
 
  Successfully ran the test case, congratulations!
 
  Successfully ran the test case, congratulations!
  
−
You can then remove the output directory if there were no errors.
+
You can remove the output directory if there were no errors.
 
  rm -rf ~/testsnp
 
  rm -rf ~/testsnp

Revision as of 15:33, 8 August 2013

Back to parent: GotCloud

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.


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

Where to Find It

On github, https://github.com/statgen/gotcloud, you can both browse and download the gotcloud source code as well as explore the history of changes.

You can obtain the source either with or without git.


Using Git To Track the Current Development Version

Clone (get your own copy)

You can create your own git clone (copy) using: 

git clone https://github.com/statgen/gotcloud.git

or 

git clone git://github.com/statgen/gotcloud.git

Either of these commands create a directory called gotcloud in the current directory.

Then just cd gotcloud and compile.

Get the latest Updates (update your copy)

To update your copy to the latest version (a major advantage of using git):

  1. cd pathToYourCopy/gotcloud
  2. make clean
  3. git pull
  4. make all

Git Refresher

If you decide to use git, but need a refresher, see How To Use Git or Notes on how to use git (if you have access)


Downloading From GitHub Without Git

If you download the latest code/version, make sure you periodically update it by downloading a newer version.

From github you can download:

  1. Latest Code (master branch)
    via Website
    1. Goto: https://github.com/statgen/gotcloud
    2. Click on the Download ZIP button on the right side panel.
    via Command Line
    wget https://github.com/statgen/gotcloud/archive/master.tar.gz
    or
    wget https://github.com/statgen/gotcloud/archive/master.zip
  2. Specific Release (via a tag)
    via Website
    1. Goto: https://github.com/statgen/gotcloud/releases to see the available releases
    2. Click zip or tar.gz for the desired version.
    via Command Line
    wget https://github.com/statgen/gotcloud/archive/<tagName>.tar.gz
    or
    wget https://github.com/statgen/gotcloud/archive/<tagName>.zip
  3. Latest Release (via a branch)
    via Website
    1. Goto: https://github.com/statgen/gotcloud/tree/latest to see the latest release
    2. Click on the Download ZIP button on the right side panel.
    via Command Line
    wget https://github.com/statgen/gotcloud/archive/latest.tar.gz
    or
    wget https://github.com/statgen/gotcloud/archive/latest.zip

After downloading the file, uncompress (unzip/untar) it. The directory created will be named gotcloud-<name of version you downloaded>.



If compilation fails due to warnings being treated as errors, please contact us so we can fix the warnings. As a work-around to get it to compile, you can disable the treatment of warnings as errors by editing libStatGen/general/Makefile to remove -Werror.

Releases

Released Versions are documented at GotCloud: Versions with details on the changes for each version.


Building

Prior to running gotcloud, you need to compile the source.

  1. cd into the gotcloud directory you just created (via clone/unzip/untar)
  2. Build (compile) the source 
    cd src; make; cd ..
    • Note: as the source builds, many messages will scroll through your terminal. You may even see some warnings. These messages are normal and expected. As long as the build does not end with an error, you have successfully built the source.

GotCloud Script

The gotcloud script that is the gateway to running GotCloud is found in the directory you created via clone/unzip/untar and is called gotcloud.

If you cloned into your home directory, it would be: 

~/gotcloud/gotcloud

If you downloaded "latest" into your home directory, it would be: 

~/gotcloud-latest/gotcloud


Testing GotCloud

You can run an automated test that will tell you if it passes or fails.

This test will ensure that everything is setup/installed properly and the expected results are produced.

Test the aligner

The aligner test takes about 3 minutes +/- 1 minute.

To run: 

~/gotcloud/gotcloud align --test ~/testalign
  • replace the beginining ~/ with the actual path to where you downloaded gotcloud
  • replace ~/testalign with the directory where you want the test results to go

Output you should see something like: 

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 '/home/myuser/gotcloud/test/align/expected/aligntest'
Successfully ran the test case, congratulations!

You can remove the output directory if there were no errors. 

rm -rf ~/testalign

Test snp calling

The snp calling test takes about 7 minutes +/- 2 minutes.

To run, replace ~/testsnp with the directory where you want the test results to go: 

~/gotcloud/gotcloud snpcall --test ~/testsnp
  • replace the beginining ~/ with the actual path to where you downloaded gotcloud
  • replace ~/testsnp with the directory where you want the test results to go

Output you should see something like: 

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 '/home/myuser/gotcloud/test/umake/expected/umaketest'
Successfully ran the test case, congratulations!

You can remove the output directory if there were no errors. 

rm -rf ~/testsnp
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