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Casey Dunn committed 42d4ee5

updated third party details

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 ## Installing dependencies
 
-The only dependencies for Agalma are BioLite and its dependencies. Please see
+Agalma relies on BioLite for many core functions. 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) 
+file for instructions on how to install BioLite. Use the method (eg, git or tarball) 
 and version that matches your Agalma installation strategy.
 
+We recommend installing the required third-party 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