From c788e9089efa7ba6971846b5cdd724b2d8e90e26 Mon Sep 17 00:00:00 2001
From: Calvin <calvin@EESI>
Date: Wed, 15 May 2013 12:43:40 -0400
Subject: change links to work for github

---
 doc/README.markdown  | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 doc/index.markdown   |  8 ++++----
 doc/install.markdown | 47 -----------------------------------------------
 3 files changed, 51 insertions(+), 51 deletions(-)
 create mode 100644 doc/README.markdown
 delete mode 100644 doc/install.markdown

diff --git a/doc/README.markdown b/doc/README.markdown
new file mode 100644
index 0000000..82004aa
--- /dev/null
+++ b/doc/README.markdown
@@ -0,0 +1,47 @@
+# How Can I Install The Quikr Utility? #
+To use Quikr there are several prerequisites. 
+
+## Requirements ##
++ Mac OS X 10.6.8 or GNU/Linux
++ 4Gb of RAM minimum. Absolutely neccessary.
++ gcc that supports OpenMP
+
+### Python Requirements ###
++ Python 2.7
++ Scipy 
++ Numpy
++ BioPython
+
+### Mac Requirements ###
++ Mac OS X 10.6.8 (what we have tested)
++ GCC 4.7 or newer. (gcc 4.2 did not work, and is the default installation)
++ OCaml compiler mlton
++ OpenMP libraries (libgomp, usually comes with gcc)
+
+### Linux Requirements ###
++ GCC 4.7 or newer
++ OCaml compiler mlton
++ OpenMP libraries (libgomp, usually comes with gcc)
+
+We also have a Quikr implementation in Matlab so that you can easily integrate
+Quikr into your custom programs and scripts.
+
+### Installation ###
+Our Quikr code is available on our sourceforge download page:
+
+[http://sourceforge.net/projects/quikr/](sourceforge project page)
+
+Our development GIT repository is available here:
+
+[http://rosalind.ece.drexel.edu/git/quikr/](rosalind.ece.drexel.edu/git/quikr/)
+
+To install quikr, download our project and in the folder run:
+
+    make
+    sudo make install
+
+This will install the quikr, quikr\_train and multifasta\_to\_otu utilities.
+To install the python scripts and module systemwide, run
+
+    make python
+    sudo make install_python
diff --git a/doc/index.markdown b/doc/index.markdown
index 03672cd..1aad66b 100644
--- a/doc/index.markdown
+++ b/doc/index.markdown
@@ -11,15 +11,15 @@ accurate down to the genus level.
 
 
 ## How Do I Install Quikr ##
-Please read the directions on the [installation page](install.html).
+Please read the directions on the [installation page](install.markdown).
 
 ## How Do I use Quikr ## 
 We have several ways to use quikr. Quikr is first and formost a command
 line utility, but we also provide python and matlab scripts.
 
-+ [Command Line Utilities](cli.html)
-+ [Matlab documentation](matlab.html)
-+ [Python documentation](python.html)
++ [Command Line Utilities](cli.markdown)
++ [Matlab documentation](matlab.markdown)
++ [Python documentation](python.markdown)
 
 ## Contact ##                                   
 For issues with the quikr software, contact gailro@gmail.com
diff --git a/doc/install.markdown b/doc/install.markdown
deleted file mode 100644
index 82004aa..0000000
--- a/doc/install.markdown
+++ /dev/null
@@ -1,47 +0,0 @@
-# How Can I Install The Quikr Utility? #
-To use Quikr there are several prerequisites. 
-
-## Requirements ##
-+ Mac OS X 10.6.8 or GNU/Linux
-+ 4Gb of RAM minimum. Absolutely neccessary.
-+ gcc that supports OpenMP
-
-### Python Requirements ###
-+ Python 2.7
-+ Scipy 
-+ Numpy
-+ BioPython
-
-### Mac Requirements ###
-+ Mac OS X 10.6.8 (what we have tested)
-+ GCC 4.7 or newer. (gcc 4.2 did not work, and is the default installation)
-+ OCaml compiler mlton
-+ OpenMP libraries (libgomp, usually comes with gcc)
-
-### Linux Requirements ###
-+ GCC 4.7 or newer
-+ OCaml compiler mlton
-+ OpenMP libraries (libgomp, usually comes with gcc)
-
-We also have a Quikr implementation in Matlab so that you can easily integrate
-Quikr into your custom programs and scripts.
-
-### Installation ###
-Our Quikr code is available on our sourceforge download page:
-
-[http://sourceforge.net/projects/quikr/](sourceforge project page)
-
-Our development GIT repository is available here:
-
-[http://rosalind.ece.drexel.edu/git/quikr/](rosalind.ece.drexel.edu/git/quikr/)
-
-To install quikr, download our project and in the folder run:
-
-    make
-    sudo make install
-
-This will install the quikr, quikr\_train and multifasta\_to\_otu utilities.
-To install the python scripts and module systemwide, run
-
-    make python
-    sudo make install_python
-- 
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