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GotCloud: Source Releases (view source)

Revision as of 15:33, 8 August 2013

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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]].
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Tar versions of gotcloud can be downloaded from github.
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= Where to Find It =
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You can download either a specific release, the latest release, or the current development version.
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{{ToolGitRepo|repoName=gotcloud|nolibStatGen=true|noDownload=true|latestReleaseBranch=latest|skipBuild=true}}
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===Downloading a specific release===
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== Releases ==
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Released Versions are documented at [[GotCloud: Versions]] with details on the changes for each version.
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See https://github.com/statgen/gotcloud/releases for the list of specific releases that can be downloaded.
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You can download by:
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= Building =
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* Selecting the <code>zip</code> or <code>tar.gz</code> button near the version.
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Prior to running gotcloud, you need to compile the source.
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* Using wget to pull it directly:
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===Downloading the latest release===
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# cd into the gotcloud directory you just created (via clone/unzip/untar)
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We track the latest release using a branch called <code>latest</code>.
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The commandline for downloading this branch is:
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=== Downloading the current development version===
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If you are using the current development, I'd recommend using git.
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== Previous GotCloud Versions ==
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You can access previous gotcloud versions using the git tags by either directly downloading the previous version or by using git to set the view to a specific tag.
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See [[GotCloud: Versions]] for details on the changes for each version.
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== Downloading & Building GotCloud ==
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Here are the steps for installing from the source tar:
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# Create & change to the directory where you want gotcloud installed
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#: <pre>cd ~    # Replace ~ with the location where you want gotcloud installed.</pre>
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# Download the gotcloud tar from the ftp site.
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#: <pre>wget ftp://share.sph.umich.edu/gotcloud/gotcloudWithTest_latest.tgz</pre>
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# Extract the tar (In this example, it is the tar with the test files)
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#: <pre>tar xzf gotcloud_latest.tgz</pre>
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#* This will create a gotcloud directory containing the contents of the tar.
   
# Build (compile) the source
 
# Build (compile) the source
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#: <pre>cd gotcloud/src; make; cd ..</pre>
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#: <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.
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= GotCloud Script =
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GotCloud requires the following tools to be installed. 
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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.
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* java (java-common default-jre on ubuntu)
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* make (make on ubuntu)
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* libssl (libssl0.9.8 on ubuntu)
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* gcc 4.4 or newer
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To check these requirements, run:
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If you cloned into your home directory, it would be:
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  scripts/check_requirements.sh .
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  ~/gotcloud/gotcloud
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If you downloaded "latest" into your home directory, it would be:
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~/gotcloud-latest/gotcloud
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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:
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gotcloud/gotcloud
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If you downloaded and untarred into your home directory, it would be:
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~/gotcloud/gotcloud
      
== Testing GotCloud ==
 
== Testing GotCloud ==
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If you installed the test files, you can run an automated test that will tell you if it passes or fails.
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You can run an automated test that will tell you if it passes or fails.
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This test will ensure that everything is setup/installed properly and produces the expected results.
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This test will ensure that everything is setup/installed properly and the expected results are produced.
    
=== Test the aligner ===
 
=== Test the aligner ===
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  Successfully ran the test case, congratulations!
 
  Successfully ran the test case, congratulations!
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You can then remove the output directory if there were no errors.
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You can remove the output directory if there were no errors.
 
  rm -rf ~/testalign
 
  rm -rf ~/testalign
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  Successfully ran the test case, congratulations!
 
  Successfully ran the test case, congratulations!
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You can then remove the output directory if there were no errors.
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You can remove the output directory if there were no errors.
 
  rm -rf ~/testsnp
 
  rm -rf ~/testsnp
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/8087"

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