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+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).
+
+.. _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:
+
+  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:
+
+  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|_.
+
+.. |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|_.
+
+.. |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/
+
+Wrapper authors: Jim Johnson
+