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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]].
= Where to Find the GotCloud Source =
{{ToolGitRepo|repoName=gotcloud|nolibStatGen=true|noDownload=true|latestReleaseBranch=latest|skipBuild=true}}
#: <pre>wget ftp://share.sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz</pre>
== Releases ==
# Extract the tar (In this example, it is the tar with the test files)
Released Versions are documented at [[GotCloud: Versions]] with details on the changes for each version.
#: <pre>tar xzf gotcloud_latest.tgz</pre>
= 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.
#: <pre>scripts/check_requirements.sh</pre>
# Build (compile) the source
# Build (compile) the source
#: <pre>cd gotcloud/src; make; cd ..</pre>
#: <pre>cd src; make; cd ..</pre>
#* 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.
#* 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 =
GotCloud requires the following tools to be installed.
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 ==
== 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 produces the expected results.
This test will ensure that everything is setup/installed properly and the expected results are produced.
=== Test the aligner ===
=== Test the aligner ===
The aligner test takes about 2 minutes +/- 1 minute.
The aligner test takes about 3 minutes +/- 2 minute.
To run:
To run:
gotcloud align --test ~/testalign
~/gotcloud/gotcloud align --test ~/testalign
* add the path to gotcloud if necessary
* 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:
Output you should see something like:
Removing any previous results from: /home/myuser/testalign/aligntest
Removing any previous results from: /home/myuser/testalign/aligntest
Running GOTCLOUD TEST, test log in: /home/myuser/testalign/aligntest.log
Running GOTCLOUD TEST, test log in: /home/myuser/testalign/aligntest.log
Processing finished in 63 secs with no errors reported
Processing finished in 63 secs with no errors reported
Results from DIFF will be in /home/myuser/testalign/diff_logfiles_results.txt
Results from DIFF will be in /home/myuser/testalign/diff_logfiles_results.txt
Successful comparison of data in '/home/myuser/testalign/aligntest' and '/usr/local/gotcloud/test/align/expected/aligntest'
Successful comparison of data in '/home/myuser/testalign/aligntest' and '/home/myuser/gotcloud/test/align/expected/aligntest'
Successfully ran the test case, congratulations!
Successfully ran the test case, congratulations!
You can then remove the output directory if there were no errors.
You can remove the output directory if there were no errors.
rm -rf ~/testalign
rm -rf ~/testalign
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:
gotcloud snpcall --test ~/testsnp
~/gotcloud/gotcloud snpcall --test ~/testsnp
* add the path to gotcloud if necessary
* 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:
Output you should see something like:
Removing any previous results from: /home/myuser/testsnp/umaketest
Removing any previous results from: /home/myuser/testsnp/umaketest
Running GOTCLOUD TEST, test log in: /home/myuser/testsnp/umaketest.log
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
Results from DIFF will be in /home/myuser/testsnp/diff_logfiles_results_umake.txt
Successful comparison of data in '/home/myuser/testsnp/umaketest' and '/usr/local/gotcloud/test/umake/expected/umaketest'
Successful comparison of data in '/home/myuser/testsnp/umaketest' and '/home/myuser/gotcloud/test/umake/expected/umaketest'
Successfully ran the test case, congratulations!
Successfully ran the test case, congratulations!
You can then remove the output directory if there were no errors.
You can remove the output directory if there were no errors.
rm -rf ~/testsnp
rm -rf ~/testsnp
