updated install section

installation/index.md

@@ -3,9 +3,11 @@ layout: templ
 title: Installation
 ---
 
-Getting the code
+Installation
 ---
 
+### Getting the code
+
 You can either download a specific version of NGSUtils or clone our Git repository. If you have `git` installed on
 your computer, this is the recommended method for installation.
 
@@ -18,42 +20,62 @@ Go to: [https://github.com/ngsutils/ngsutils/tags](https://github.com/ngsutils/n
 The easiest way to install (and get updates) is to checkout the code from GitHub directly. To do this, you'll need
 to clone our repository.
 
-`git clone git://github.com/ngsutils/ngsutils.git`
 
+#### Install/compile dependencies
 
-Installation
----
+```
+$ git clone git://github.com/ngsutils/ngsutils.git
+$ cd ngsutils
+$ make
+```
 
 Once you have the code downloaded, you need to run `make` in the ngsutils directory. This will create a virtualenv folder
-(env) and install the needed libraries. Once you run `make`, you should be able to run the `bamutils`, `bedutils`, 
+(venv) and install the needed libraries. Once you run `make`, you should be able to run the `bamutils`, `bedutils`, 
 `fastqutils`, and `gtfutils` programs. It is often helpful to add these files to your $PATH so that you can call them
 directly without entering their full pathnames.
 
+
+##### Custom python interpreter
+
+If you need to use a custom python interpreter, such as `python2.6`, then you can specify this at the command line before running `make`.
+The given interpreter will be used to create the virtualenv environment and be used by NGSUtils in the future without needing to specify the
+PYTHON variable.
+
+```
+$ PYTHON=python2.6 make
+```
+
 ### Requirements
 
 
 #### Requires
 
 * Mac OSX or Linux operating system (tested on RHEL5 and RHEL6)
 * Python 2.6+ (including development packages)
-* [virtualenv](http://www.virtualenv.org/)
 * Make
 
+
 > Note: for RHEL5, it is recommended that you add the EPEL repository to your yum configuration and 
-> install the python26 and python26-virtualenv packages. This will let NGSUtils use the proper version of Python
+> install the python26 packages. This will let NGSUtils use the proper version of Python
 > without disrupting any system utilities.
+>
+> Also, virtualenv is now bundled with NGSUtils to make installation easier.
 
 #### Will install
 
 * [pysam](http://wwwfgu.anat.ox.ac.uk/~andreas/documentation/samtools/contents.html)
 * Cython
+* [swalign](http://github.com/mbreese/swalign)
+* [eta](http://github.com/mbreese/eta) (progress bars for terminal; hidden when run in pipelines)
+* coverage
 
-The only libraries that are mandatory are *pysam* and *cython*. Additionally, Cython requires that the
-Python headers be present on the system. For a linux system this can be achieved by installing
-'python-devel' or similar. These will both be installed in the virtualenv env folder.
+Additionally, Cython requires that the Python headers be present on the system. For a linux 
+system this can be achieved by installing 'python-devel' or similar.
 
 #### Recommended
 
+Here are some other tools that NGSUtils will work with.
+
 * [samtools](http://samtools.sourceforge.net/) (indexing BAM/FASTA files)
 * tabix (indexing tab-delimited BED files)