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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
author iuc
date Tue, 18 Apr 2017 09:33:56 -0400
parents 500832f27cbc
children ce135864629c
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4 These are galaxy tools for SnpEff_, a variant annotation and effect prediction tool by Pablo Cingolani. 4 These are galaxy tools for SnpEff_, a variant annotation and effect prediction tool by Pablo Cingolani.
5 It annotates and predicts the effects of variants on genes (such as amino acid changes). 5 It annotates and predicts the effects of variants on genes (such as amino acid changes).
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7 .. _SnpEff: http://snpeff.sourceforge.net/ 7 .. _SnpEff: http://snpeff.sourceforge.net/
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10 This repository let you automatically install SnpEff and SnpSift.
11 This will use the default location for genome reference downloads from the ``snpEff.config`` file:
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13 data_dir = ~/snpEff/data/
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15 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``.
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17 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. 9 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.
18 You can fill this file by running the following command: 10 You can fill this file by running the following command:
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20 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 12 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
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34 .. |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 26 .. |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
35 .. _Cingolani2012using: http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00035/ 27 .. _Cingolani2012using: http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00035/
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37 Wrapper authors: Jim Johnson 29 Wrapper authors: Jim Johnson
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