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):
cd pathToYourCopy/gotcloud
make clean
git pull
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:
- Latest Code (master branch)
- via Website
- Goto: https://github.com/statgen/gotcloud
- Click on the
Download ZIP
button on the right side panel.
- via Command Line
- via Website
- Specific Release (via a tag)
- via Website
- Goto: https://github.com/statgen/gotcloud/releases to see the available releases
- Click
zip
ortar.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
- via Website
- Latest Release (via a branch)
- via Website
- Goto: https://github.com/statgen/gotcloud/tree/latest to see the latest release
- Click on the
Download ZIP
button on the right side panel.
- via Command Line
- via Website
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.
- cd into the gotcloud directory you just created (via clone/unzip/untar)
- Check that your system has all of the requirements. Install whatever is needed.
scripts/check_requirements.sh
- 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