GotCloud: Source Releases
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.
Tar versions of gotcloud can be downloaded from github.
You can download either a specific release, the latest release, or the current development version.
Downloading a specific release
See https://github.com/statgen/gotcloud/releases for the list of specific releases that can be downloaded.
You can download by:
- Selecting the
zip
ortar.gz
button near the version. - Using wget to pull it directly:
Downloading the latest release
We track the latest release using a branch called latest
.
The commandline for downloading this branch is:
Downloading the current development version
If you are using the current development, I'd recommend using git.
Previous GotCloud Versions
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.
See GotCloud: Versions for details on the changes for each version.
Downloading & Building GotCloud
Here are the steps for installing from the source tar:
- Create & change to the directory where you want gotcloud installed
cd ~ # Replace ~ with the location where you want gotcloud installed.
- Download the gotcloud tar from the ftp site.
wget ftp://share.sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz
- Extract the tar (In this example, it is the tar with the test files)
tar xzf gotcloud_latest.tgz
- This will create a gotcloud directory containing the contents of the tar.
- Build (compile) the source
cd gotcloud/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 requires the following tools to be installed.
- java (java-common default-jre on ubuntu)
- make (make on ubuntu)
- libssl (libssl0.9.8 on ubuntu)
- gcc 4.4 or newer
To check these requirements, run:
scripts/check_requirements.sh .
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
If you downloaded and untarred into your home directory, it would be:
~/gotcloud/gotcloud
Testing GotCloud
If you installed the test files, 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.
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 then 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 then remove the output directory if there were no errors.
rm -rf ~/testsnp