comparison readme.rst @ 7:7adfd0589f49 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1

6:20f0429a4bfe

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

.. |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

7:7adfd0589f49

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/

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

.. |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