Difference between revisions of "GotCloud: Source Releases"
Line 15: | Line 15: | ||
Here are the steps for installing from the source tar: | Here are the steps for installing from the source tar: | ||
# Create & change to the directory where you want gotcloud installed | # Create & change to the directory where you want gotcloud installed | ||
− | #: <pre> | + | #: <pre>cd ~ # Replace ~ with the location where you want gotcloud installed.</pre> |
# Download the gotcloud tar from the ftp site. | # Download the gotcloud tar from the ftp site. | ||
#: <pre>wget ftp://share.sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz</pre> | #: <pre>wget ftp://share.sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz</pre> | ||
Line 36: | Line 36: | ||
− | The gotcloud | + | 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 | gotcloud/gotcloud | ||
+ | If you downloaded and untarred into your home directory, it would be: | ||
+ | ~/gotcloud/gotcloud | ||
== Testing GotCloud == | == Testing GotCloud == | ||
Line 49: | Line 51: | ||
To run: | To run: | ||
− | gotcloud align --test ~/testalign | + | ~/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 | * replace ~/testalign with the directory where you want the test results to go | ||
− | 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 | ||
Line 62: | Line 64: | ||
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 '/ | + | 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! | ||
Line 73: | Line 75: | ||
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 |
− | * | + | * 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 | ||
− | 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 '/ | + | 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 then remove the output directory if there were no errors. | ||
rm -rf ~/testsnp | rm -rf ~/testsnp |
Revision as of 17:09, 19 March 2013
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:
- both the gotcloud programs/source and the test files
- just the gotcloud programs/source
- just the gotcloud test files
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 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 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
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