Updated installation documentation.

doc/source/installation.rst

 Installation
 ==============
+Installation is made much easier by using the pre-built
+`anaconda <https://anaconda.org/>`_ packages.  There are two different packages
+located under the `hcc channel <https://anaconda.org/hcc>`_.
+The chipathlon package contains all software necessary to run & generate
+workflows.  The chipathlon-client packages contains all software necessary to
+generate workflows with the expectation that the execute host has the
+necessary software installed.  idr uses python3 however, so it must be
+created in a separate environment.  Once you have conda installed:
+
+.. code-block:: bash
+
+  # Add the required channels for all software
+  conda config --add channels conda-forge
+  conda config --add channels r
+  conda config --add channels HCC
+  conda config --add channels bioconda
+  # Create the chip env with all software except idr
+  conda create -n chip python=2.7 chipathlon
+  # Create the idr environment
+  conda create -n idr python=3.5 idr
+
+This will create the two environments necessary to run workflows.  The chip
+environment can also be used to generate and submit workflows:
+
+.. code-block:: bash
+
+  # Activate chip env
+  source activate chip
+  # Generate the workflow
+  chip-gen...
+
+Below is the full list of dependencies if you don't want to use conda.
+
+Dependencies
+^^^^^^^^^^^^
+
+**Dependencies for chipathlon**
 
-Dependencies for chipathlon
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 * `Pegasus <http://pegasus.isi.edu/>`_
 * `pymongo <https://api.mongodb.com/python/current/>`_
 * `yaml <http://pyyaml.org/>`_
 
-Dependencies for running workflows
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+**Dependencies for running workflows**
+
 * `Gem <http://groups.csail.mit.edu/cgs/gem/>`_
 * `Zerone <https://omictools.com/zerone-tool>`_
 * `MACS2 <https://github.com/taoliu/MACS>`_
@@ -22,9 +57,23 @@ Dependencies for running workflows
 * `picard <https://github.com/pezmaster31/bamtools>`_
 * `bwa <http://bio-bwa.sourceforge.net>`_
 * `bowtie2 <http://bowtie-bio.sourceforge.net/bowtie2/index.shtml>`_
+* `idr <https://github.com/nboley/idr>`_
+
+**Dependencies for building docs**
 
-Dependencies for building docs
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 * `Sphinx <http://www.sphinx-doc.org/en/stable/>`_
 * `Sphinx Argparse <https://github.com/ribozz/sphinx-argparse>`_
 * `Read the Docs Theme <https://github.com/rtfd/sphinx_rtd_theme>`_
+
+Setting up bosco
+^^^^^^^^^^^^^^^^^
+To use bosco with the chipathlon-client package a small amount of setup must
+be done first.  Namely, adding the target cluster that you wish to use.
+This can be done with the following command:
+
+.. code-block:: bash
+
+  bosco_cluster -a USERNAME@HOST.org slurm
+
+This will generate and copy ssh keys that will be used to transfer files
+between your submit host and your execute host.