From Genome Analysis Wiki
Revision as of 15:37, 8 August 2013 by Mktrost (talk | contribs)
Jump to: navigation, search

The {{{repoName}}} repository is available both via release downloads and via github.

On github, https://github.com/statgen/{{{repoName}}}, you can both browse and download the {{{repoName}}} source code as well as explore the history of changes.

You can obtain the source either with or without git.

The releases may be available both with and without libStatGen included.

If you do not use the release version that already contains libStatGen, you need to download the library: libStatGen.

If you try to compile {{{repoName}}} and it cannot find libStatGen, it will fail and provide instructions of what to do next:

  • if libStatGen is in a different location then expected
    • follow the directions to set the path to libStatGen
  • if libStatGen is not downloaded and you have git
    • make libStatGen will download via git and build libStatGen
  • if libStatGen is not downloaded and you don't have git

Using Git To Track the Current Development Version

Clone (get your own copy)

You can create your own git clone (copy) using:

git clone https://github.com/statgen/{{{repoName}}}.git


git clone git://github.com/statgen/{{{repoName}}}.git

Either of these commands create a directory called {{{repoName}}} in the current directory.

Then just cd {{{repoName}}} and compile.

Get the latest Updates (update your copy)

To update your copy to the latest version (a major advantage of using git):

  1. cd pathToYourCopy/{{{repoName}}}
  2. make clean
  3. git pull
  4. make all

Git Refresher

If you decide to use git, but need a refresher, see How To Use Git or Notes on how to use git (if you have access)

Downloading From GitHub Without Git

If you download the latest code/version, make sure you periodically update it by downloading a newer version.

From github you can download:

  1. Latest Code (master branch)
    via Website
    1. Goto: https://github.com/statgen/{{{repoName}}}
    2. Click on the Download ZIP button on the right side panel.
    via Command Line
    wget https://github.com/statgen/{{{repoName}}}/archive/master.tar.gz
    wget https://github.com/statgen/{{{repoName}}}/archive/master.zip
  2. Specific Release (via a tag)
    via Website
    1. Goto: https://github.com/statgen/{{{repoName}}}/releases to see the available releases
    2. Click zip or tar.gz for the desired version.
    via Command Line
    wget https://github.com/statgen/{{{repoName}}}/archive/<tagName>.tar.gz
    wget https://github.com/statgen/{{{repoName}}}/archive/<tagName>.zip

After downloading the file, uncompress (unzip/untar) it. The directory created will be named {{{repoName}}}-<name of version you downloaded>.


After obtaining the {{{repoName}}} repository (either by download or from github), compile the code using:

make all  

Object (.o) files are compiled into the obj directory with a subdirectory debug and profile for the debugging and profiling objects.

This creates the executable(s) in the {{{repoName}}}/bin/ directory, the debug executable(s) in the {{{repoName}}}/bin/debug/ directory, and the profiling executable(s) in the {{{repoName}}}/bin/profile/ directory.

make install installs the opt binary if you have permission.

make test compiles for opt, debug, and profile and runs the tests (found in the test subdirectory).

To see all make options, type make help.