GotCloud: Source Releases

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The GotCloud software has been developed and tested on Linux Ubuntu 13.10, 13.04, 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 the GotCloud Source

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. Check that your system has all of the requirements. Install whatever is needed.

   scripts/check_requirements.sh

3. 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 +/- 2 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
• To test the software in a cluster environment add the option -batchtype. For instance, using Sun Grid Engine in a Starcluster cluster, use

~/gotcloud/gotcloud align --test ~/testalign -batchtype sgei

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 5 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
• To test the software in a cluster environment add the option -batchtype. For instance, using Sun Grid Engine in a Starcluster cluster, use

~/gotcloud/gotcloud snpcall --test ~/testsnp -batchtype sgei

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