Difference between revisions of "GotCloud: Source Releases"

From Genome Analysis Wiki
Jump to navigationJump to search
Line 3: Line 3:
 
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 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 can be downloaded from:
+
There are 3 tar files that can be downloaded:
−
ftp://share.sph.umich.edu/gotcloud/gotcloud_latest.tgz
+
# both the gotcloud programs/source and the test files
 +
#:ftp://share.sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz
 +
# just the gotcloud programs/source
 +
#:ftp://share.sph.umich.edu/gotcloud/gotcloud_latest.tgz
 +
# just the gotcloud test files
 +
#:ftp://share.sph.umich.edu/gotcloud/gotcloudTest_latest.tgz
 +
 
 +
== Downloading & Building GotCloud ==
  
 
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>mkdir -p $GCHOME; cd $GCHOME    # Replace $GCHOME with the location where you want it installed.</pre>
 
# Download the gotcloud tar from the ftp site.
 
# Download the gotcloud tar from the ftp site.
−
# Extract the tar
+
#: <pre>wget ftp://share.sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz</pre>
 +
# Extract the tar (In this example, it is the tar with the test files)
 +
#: <pre>tar xzf gotcloud_latest.tgz</pre>
 +
#* This will create a gotcloud directory containing the contents of the tar.
 
# Build (compile) the source
 
# Build (compile) the source
 +
#: <pre>cd gotcloud/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.
  
−
mkdir -p $GCHOME; cd $GCHOME    # Replace $GCHOME with the location where you want it installed.
 
−
wget ftp://share.sph.umich.edu/gotcloud/gotcloud_latest.tgz  # Download
 
−
tar xzf gotcloud_latest.tgz    # Extract
 
−
cd gotcloud/src; make; cd ..    # Build source
 
 
   
 
   
 
GotCloud requires the following tools to be installed.   
 
GotCloud requires the following tools to be installed.   
Line 26: Line 34:
 
To check these requirements, run:
 
To check these requirements, run:
 
  scripts/check_requirements.sh .
 
  scripts/check_requirements.sh .
 +
 +
 +
The gotcloud scrip 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
 +
 +
== 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 align --test ~/testalign
 +
* add the path to gotcloud if necessary
 +
* replace ~/testalign with the directory where you want the test results to go
 +
 +
Output you should see:
 +
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 '/usr/local/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 snpcall --test ~/testsnp
 +
* add the path to gotcloud if necessary
 +
* replace ~/testsnp with the directory where you want the test results to go
 +
 +
Output you should see:
 +
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 '/usr/local/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

Revision as of 13:13, 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:

  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

Downloading & Building GotCloud

Here are the steps for installing from the source tar:

  1. Create & change to the directory where you want gotcloud installed 
    mkdir -p $GCHOME; cd $GCHOME    # Replace $GCHOME with the location where you want it 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 scrip 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

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 align --test ~/testalign
  • add the path to gotcloud if necessary
  • replace ~/testalign with the directory where you want the test results to go

Output you should see: 

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 '/usr/local/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 snpcall --test ~/testsnp
  • add the path to gotcloud if necessary
  • replace ~/testsnp with the directory where you want the test results to go

Output you should see: 

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 '/usr/local/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
Retrieved from "http://genome.sph.umich.edu/w/index.php?title=GotCloud:_Source_Releases&oldid=6833"