Casey Dunn committed 42d4ee5

updated third party details

  • Participants
  • Parent commits ada1e8c
  • Branches release-0.4.0

Comments (0)

Files changed (1)

 ## 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]( 
-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](, 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/ 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