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Casey Dunn committed ada1e8c

INSTALL.md streamlined

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 Python modules:
 
-* [biolite 0.4.0 or development branch](https://bitbucket.org/caseywdunn/biolite)
-* networkx >=1.6
+* [biolite](https://bitbucket.org/caseywdunn/biolite), the release version or 
+  development branch must match that of Agalma
 
 Third-party tools called from Agalma, which need to be in your PATH:
 
 
 ## Installing dependencies
 
-### Python modules
+The only dependencies for Agalma are BioLite and its dependencies. Please see
+the BioLite [INSTALL](https://bitbucket.org/caseywdunn/biolite/src/master/INSTALL.md) 
+file for instructions on how to install these. Use the method (eg, git or tarball) 
+and version that matches your Agalma installation strategy.
 
-On **Linux**:
-
-    sudo pip install networkx
-
-On **OS X**, we recommend installing to your user directory so you don't need sudo:
-
-    pip install --user networkx
-
-Then install the corresponding tarball or git branch for BioLite. For instance,
-if you are installing Agalma release 0.4.0, then download the tarball for BioLite
-release 0.4.0 and run:
-
-    tar xf biolite-0.4.0.tar.gz
-    cd biolite-0.4.0
-    python setup.py install
-
-To install a development branch of Agalma, you would also install the
-corresponding branch in BioLite. For instance, to install the release testing
-branch `release-0.4.0`, run:
-
-    git clone https://bitbucket.org/caseywdunn/biolite.git
-    cd biolite
-    git checkout release-0.4.0
-    python setup.py install
-
-To install a feature branch of Agalma, e.g. `issue-112`, prepend `agalma-` for
-the corresponding branch in BioLite, e.g. `agalma-issue-112`:
-
-    git clone https://bitbucket.org/caseywdunn/biolite.git
-    cd biolite
-    git checkout agalma-issue-112
-    python setup.py install
-
-
-### Third-party tools
-
-We recommend installing these tools using
-[Bioinformatics Brew](http://bib.bitbucket.org), a cross-platform package manager
-for bioinformatics tools. Once BiB is installed, run:
-
-    bib install -f biolite-tools/0.4.0 blast/2.2.29+ bowtie/1.0.0 bowtie2/2.1.0 fastqc/0.10.1 gblocks/0.91b mafft/7.130 mcl/12-135 parallel/20130922 raxml/7.7.6 rsem/1.2.9 samtools/0.1.19 sratoolkit/0.2.3.4-2 transdecoder/r2012-08-15 trinity/r2013_08_14
-
-For the optional tools, run:
-
-    bib install -f macse/0.9b1 oma/0.99u.3
 
 
 ## Installing Agalma from the tarball
     cd agalma-0.4.0
     python setup.py install
 
+During the install stage, the installer will download a zip file containing
+BLAST databases that have been optimized for Agalma.
+
 For an alternate install path, specify a prefix with:
 
     python setup.py install --prefix=...
     cd agalma
     python setup.py install
 
-If you install from the git repo, you need to obtain a copy of the BLAST databases
-that are packaged in the tarball. Either download the tarball and copy the
-`agalma/blastdb` directory into your repo tree, or follow the instructions in the
-next section to generate the BLAST databases from scratch.
+If you edit the code in the repository, or pull a new version, then run the following 
+to update the installation:
+
+    python setup.py install
 
 
 ## Generating a tarball from the git repo