diff readme.rst @ 11:c5288d5a446e

Update to version 3.6 and refactor to new repositories: snpsift, snpeff_datatypes, data_manager_snpeff

--- a/readme.rst	Tue Dec 10 14:28:37 2013 -0600
+++ b/readme.rst	Thu Jun 26 08:40:30 2014 -0500
@@ -4,19 +4,11 @@
 
 This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift.   
 
-This will use the default location for genome reference downloads from the snpEff.config:
-data_dir = ~/snpEff/data/
-You can manually edit the installed snpEff.config 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
     "SnpEff Download" snpEff_download.xml
 are taken from: tool-data/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 
-  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 
-
 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]