--- a/readme.rst	Mon Nov 10 09:33:36 2014 -0600
+++ b/readme.rst	Tue Jan 13 13:36:11 2015 -0600
@@ -1,20 +1,38 @@
-These are galaxy tools for SnpEff a variant annotation and effect prediction tool by Pablo Cingolani. 
+SnpEff wrappers
+===============
+
+These are galaxy tools for SnpEff_, a variant annotation and effect prediction tool by Pablo Cingolani.
 It annotates and predicts the effects of variants on genes (such as amino acid changes).
-( http://snpeff.sourceforge.net/ )
+
+.. _SnpEff: http://snpeff.sourceforge.net/
+
+
+This repository let you automatically install SnpEff and SnpSift.
+This will use the default location for genome reference downloads from the ``snpEff.config`` file:
 
-This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift.   
+  data_dir = ~/snpEff/data/
+
+You can manually edit the installed ``snpEff.config`` file and change the location, or you can create a symbolic link to the desired data location from ``~/snpEff``.
+
+The genome reference options used by the tools "SnpEff" (snpEff.xml) and "SnpEff Download" (snpEff_download.xml) are taken from the ``tool-data/snpeffect_genomedb.loc`` file.
+You can fill this file by running the following command:
 
-The genome reference options used by the tools:
-    "SnpEff"  snpEff.xml
-    "SnpEff Download" snpEff_download.xml
-are taken from: tool-data/snpeffect_genomedb.loc
+  java -jar snpEff.jar databases | tail -n +3 | cut -f 1,2 | awk '{ gsub(/_/, " ", $2); printf "%s\\t%s : %s\\n", $1, $2, $1 }' | sort -k 2 > snpeffect_genomedb.loc
+
+There are 2 datamanagers to download and install prebuilt SnpEff genome databases:
+
+* data_manager_snpeff_databases: generates a list of available SnpEff genome databases into the ``tool-data/snpeff_databases.loc`` file
+* data_manager_snpeff_download: downloads a SnpEff genome database selected from ``tool-data/snpeff_databases.loc`` and adds entries to ``snpeff_genomedb.loc``, ``snpeff_regulationdb.loc`` and ``snpeff_annotations.loc``
+
+SnpEff citation: |Cingolani2012program|_.
 
-There are 2 datamanagers to download and install prebuilt SnpEff Genome databases:
-  data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc 
-  data_manager_snpeff_download - downloads a SnpEff genome database selected from: tool-data/snpeff_databases.loc and adds entries to snpeff_genomedb.loc,snpeff_regulationdb.loc,snpeff_annotations.loc 
+.. |Cingolani2012program| replace:: Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., Ruden, D. M. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of *Drosophila melanogaster* strain w1118; iso-2; iso-3. *Fly* 6(2):80-92
+.. _Cingolani2012program: https://www.landesbioscience.com/journals/fly/article/19695/
+
+SnpSift citation: |Cingolani2012using|_.
 
-SnpEff citation:
-"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
+.. |Cingolani2012using| replace:: Cingolani, P., Patel, V. M., Coon, M., Nguyen, T., Land, S. J., Ruden, D. M., Lu, X. (2012) Using *Drosophila melanogaster* as a model for genotoxic chemical mutational studies with a new program, SnpSift. *Front. Genet.* 3:35
+.. _Cingolani2012using: http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00035/
 
-SnpSift citation:
-"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
+Wrapper authors: Jim Johnson
+