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Back to parent: [[GotCloud]]
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.
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, [[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]].
= Where to Find It =
= Where to Find the GotCloud Source =
{{ToolGitRepo|repoName=gotcloud|nolibStatGen=true|noDownload=true|latestReleaseBranch=latest|skipBuild=true}}
{{ToolGitRepo|repoName=gotcloud|nolibStatGen=true|noDownload=true|latestReleaseBranch=latest|skipBuild=true}}
# cd into the gotcloud directory you just created (via clone/unzip/untar)
# 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.
#: <pre>scripts/check_requirements.sh</pre>
# Build (compile) the source
# Build (compile) the source
#: <pre>cd src; make; cd ..</pre>
#: <pre>cd src; make; cd ..</pre>
=== Test the aligner ===
=== Test the aligner ===
The aligner test takes about 3 minutes +/- 1 minute.
The aligner test takes about 3 minutes +/- 2 minute.
To run:
To run:
* replace the beginining ~/ with the actual path to where you downloaded gotcloud
* 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
* 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:
Output you should see something like:
=== Test snp calling ===
=== Test snp calling ===
The snp calling test takes about 7 minutes +/- 2 minutes.
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:
To run, replace ~/testsnp with the directory where you want the test results to go:
* replace the beginining ~/ with the actual path to where you downloaded gotcloud
* 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
* 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:
Output you should see something like:
