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| -rw-r--r-- | academic/snpEff/README | 28 | ||||
| -rw-r--r-- | academic/snpEff/References | 23 | ||||
| -rw-r--r-- | academic/snpEff/slack-desc | 19 | ||||
| -rw-r--r-- | academic/snpEff/snpEff.SlackBuild | 74 | ||||
| -rw-r--r-- | academic/snpEff/snpEff.info | 10 |
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diff --git a/academic/snpEff/README b/academic/snpEff/README new file mode 100644 index 0000000000..a32c83dfba --- /dev/null +++ b/academic/snpEff/README @@ -0,0 +1,28 @@ +SnpEff: Genetic variant annotation and effect prediction toolbox + +SnpEff is a variant annotation and effect prediction tool. It +annotates and predicts the effects of variants on genes (such as amino +acid changes). + +Input: The inputs are predicted variants (SNPs, insertions, deletions +and MNPs). The input file is usually obtained as a result of a +sequencing experiment, and it is usually in variant call format (VCF). + +Output: SnpEff analyzes the input variants. It annotates the variants +and calculates the effects they produce on known genes (e.g. amino +acid changes). + +This also installs SnpSift, a toolbox that allows you to filter and +manipulate annotated files. Once your genomic variants have been +annotated, you need to filter them out in order to find the +"interesting / relevant variants". Given the large data files, this is +not a trivial task (e.g. you cannot load all the variants into XLS +spreadsheet). SnpSift helps to perform this VCF file manipulation and +filtering required at this stage in data processing pipelines. + +If you are using SnpEff or SnpSift, please cite: +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 diff --git a/academic/snpEff/References b/academic/snpEff/References new file mode 100644 index 0000000000..75b03dde80 --- /dev/null +++ b/academic/snpEff/References @@ -0,0 +1,23 @@ +f you are using SnpEff or SnpSift, please cite our work. + +Citing SnpEff: +"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 + +You can find the paper here: +http://snpeff.sourceforge.net/SnpEff_paper.pdf + +BibTex entry: + +@article{cingolani2012program, + title={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}, + author={Cingolani, P. and Platts, A. and Coon, M. and Nguyen, T. and Wang, L. and Land, S.J. and Lu, X. and Ruden, D.M.}, + journal={Fly}, + volume={6}, + number={2}, + pages={80-92}, + year={2012} +} diff --git a/academic/snpEff/slack-desc b/academic/snpEff/slack-desc new file mode 100644 index 0000000000..4c57058f93 --- /dev/null +++ b/academic/snpEff/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +snpEff: snpEff (Genetic variant annotation and effect prediction toolbox) +snpEff: +snpEff: SnpEff is a variant annotation and effect prediction tool. It +snpEff: annotates and predicts the effects of variants on genes (such +snpEff: as amino acid changes). +snpEff: +snpEff: Home: http://snpeff.sourceforge.net/ +snpEff: References: /usr/doc/snpEff-4.1b/References +snpEff: +snpEff: +snpEff: diff --git a/academic/snpEff/snpEff.SlackBuild b/academic/snpEff/snpEff.SlackBuild new file mode 100644 index 0000000000..6f0e9e41cd --- /dev/null +++ b/academic/snpEff/snpEff.SlackBuild @@ -0,0 +1,74 @@ +#!/bin/sh + +# Slackware build script for snpEff + +# Copyright 2015 Petar Petrov petar.petrov@student.oulu.fi +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=snpEff +VERSION=${VERSION:-4.1b} +SRCVER=${SRCVER:-v4_1b} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +ARCH=noarch + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM +unzip $CWD/${PRGNAM}_${SRCVER}_core.zip +cd $PRGNAM +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +mkdir -p $PKG/usr/share/java/$PRGNAM +cp -a examples galaxy scripts $PRGNAM.config $PRGNAM.jar SnpSift.jar \ + $PKG/usr/share/java/$PRGNAM + +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +ln -s ../share/java/$PRGNAM/snpEff.jar +ln -s ../share/java/$PRGNAM/SnpSift.jar +cd - + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/snpEff/snpEff.info b/academic/snpEff/snpEff.info new file mode 100644 index 0000000000..92804c89ae --- /dev/null +++ b/academic/snpEff/snpEff.info @@ -0,0 +1,10 @@ +PRGNAM="snpEff" +VERSION="4.1b" +HOMEPAGE="http://snpeff.sourceforge.net/" +DOWNLOAD="http://sourceforge.net/projects/snpeff/files/snpEff_v4_1b_core.zip" +MD5SUM="60ba0104e63aef0b8ddbd62610af328a" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="jdk" +MAINTAINER="Petar Petrov" +EMAIL="petar.petrov@student.oulu.fi" |