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.

There are 3 tar files that can be downloaded:

1. both the gotcloud programs/source and the test files

   ftp://share.sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz

2. just the gotcloud programs/source

   ftp://share.sph.umich.edu/gotcloud/gotcloud_latest.tgz

3. just the gotcloud test files

   ftp://share.sph.umich.edu/gotcloud/gotcloudTest_latest.tgz

Previous versions are also available (where M.n is the desired version number):

1. both the gotcloud programs/source and the test files

   ftp://share.sph.umich.edu/gotcloud/M.n/gotcloudWithTest_M.n.tgz

2. just the gotcloud programs/source

   ftp://share.sph.umich.edu/gotcloud/M.n/gotcloud_M.n.tgz

3. just the gotcloud test files

   ftp://share.sph.umich.edu/gotcloud/M.n/gotcloudTest_M.n.tgz

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

Downloading & Building GotCloud

Here are the steps for installing from the source tar:

1. Create & change to the directory where you want gotcloud installed

   cd ~    # Replace ~ with the location where you want gotcloud installed.

2. Download the gotcloud tar from the ftp site.

   wget ftp://share.sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz

3. 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.
4. 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 2 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