StatgenTools - Revision history

Mktrost: Add releases

2011-09-09T17:06:24Z

Add releases

← Older revision		Revision as of 13:06, 9 September 2011
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	== Where to Find It ==		== Where to Find It ==
	{{ToolGitRepo\|repoName=statgenTools}}		{{ToolGitRepo\|repoName=statgenTools}}

			== Releases ==
			Release downloads are '''Coming Soon'''.


	= Programs/Tools =		= Programs/Tools =

Mktrost: Replace the download info with the template

2011-09-09T14:35:50Z

Replace the download info with the template

@@ Line 8: / Line 8: @@
 == Where to Find It ==
-The statgenTools repository is available both via release downloads (coming soon) and via github.
+{{ToolGitRepo|repoName=statgenTools}}
 = Programs/Tools =

Mktrost: Remove statgenTools category since it is currently just one page.

2011-09-06T14:49:03Z

Remove statgenTools category since it is currently just one page.

← Older revision		Revision as of 10:49, 6 September 2011
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	~~[[Category:statgenTools]]~~
	[[Category:C++]]		[[Category:C++]]
	[[Category:Software]]		[[Category:Software]]

Mktrost: /* Programs/Tools */ add link to tool

2011-09-06T14:44:44Z

Programs/Tools: add link to tool

← Older revision		Revision as of 10:44, 6 September 2011
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	The <code>statgenTools</code> repository contains the following tools:		The <code>statgenTools</code> repository contains the following tools:

	* createUMref - Create the University of Michigan formatted reference used by many of our tools.		* [[statgenTools#createUMref\|createUMref - Create the University of Michigan formatted reference used by many of our tools.]]

Mktrost: Create statgenTools page with createUMref

2011-09-06T14:43:53Z

Create statgenTools page with createUMref

New page

[[Category:statgenTools]]
[[Category:C++]]
[[Category:Software]]

= statgenTools Overview =

statgenTools is a repository that contains programs that perform operations for our statistical genetic processing. Each program builds its own executable. This repository was created to group simple, small tools into one place. The executables will be put in the <code>bin</code> directory.

== Where to Find It ==
The statgenTools repository is available both via release downloads (coming soon) and via github.

On github, you can both browse and download the latest version of the repository as well as explore the history of changes.

You can access the latest version with or without git.

If you download from github or use git to keep up to date, you also need to download our library: [[C++ Library: libStatGen|libStatGen]].

The releases will be available both with and without libStatGen included. If you download the verison without libStatGen included, you will also need to download libStatGen separately.
(It will be available without libStatGen in case you already have a downloaded version of libStatGen that you want to use.

=== Releases ===
Release downloads are '''Coming Soon'''.

=== Using github ===

==== 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/statgenTools.git
or
git clone git://github.com/statgen/statgenTools.git

Either of these commands create a directory called <code>statgenTools</code> in the current directory.

Then just <code>cd statgenTools</code> and [[statgenTools#Building|compile]].

===== Get the latest Updates (update your copy) =====
To update your copy to the latest version (a major advantage of using git):
# <code>cd pathToYourCopy/statgenTools</code>
# <code>make clean</code>
# <code>git pull</code>
# <code>make all</code>

=== Git Refresher ===
If you decide to use git, but need a refresher, see [[How To Use Git]] or [https://statgen.sph.umich.edu/wiki/How_To_Use_Git Notes on how to use git] (if you have access)

==== Downloading From GitHub Without Git ====
Periodically download the latest copy from github from the "Downloads" link on the webpage: https://github.com/statgen/statgenTools/archives/master.

The downloaded tar file is named "statgen-statgenTools-someHexNumber.tar.gz". The directory created when it is untared shares the same base name. I recommend that you do not change the name of the directory. If you want one called statgenTools, create a link to this directory. The hex number in the directory name identifies the version of the repository that you downloaded and is necessary to easily troubleshoot any issues you encounter. If you must rename the directory, be sure to record the hex number that was on the download for future reference.

== Building ==
After obtaining the statgenTools repository (either by download or from github), compile the code using <code>make all</code>. This creates the executable all the executables in the <code>statgenTools/bin/</code> directory, the debug executables in the <code>statgenTools/bin/debug/</code> directory, and the profiling executables in the <code>statgenTools/bin/profile/</code> directory.

= Programs/Tools =

The <code>statgenTools</code> repository contains the following tools:

* createUMref - Create the University of Michigan formatted reference used by many of our tools.

These executables are built using [[C++ Library: libStatGen]].

Just running the executable with no options will print the Usage information for the executable.

== createUMref ==

Create the UM reference from the .fa file.
Usage: createUMref [--mmap] [--force] refFileName.fa
--mmap : toggle whether to use memory map (default: true)
--force: toggle whether to force creation even if it already exists