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academic/snpEff: Added (Genes toolbox).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
d0331edf8e
commit
4dec57226a
5 changed files with 154 additions and 0 deletions
28
academic/snpEff/README
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28
academic/snpEff/README
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SnpEff: Genetic variant annotation and effect prediction toolbox
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SnpEff is a variant annotation and effect prediction tool. It
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annotates and predicts the effects of variants on genes (such as amino
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acid changes).
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Input: The inputs are predicted variants (SNPs, insertions, deletions
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and MNPs). The input file is usually obtained as a result of a
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sequencing experiment, and it is usually in variant call format (VCF).
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Output: SnpEff analyzes the input variants. It annotates the variants
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and calculates the effects they produce on known genes (e.g. amino
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acid changes).
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This also installs SnpSift, a toolbox that allows you to filter and
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manipulate annotated files. Once your genomic variants have been
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annotated, you need to filter them out in order to find the
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"interesting / relevant variants". Given the large data files, this is
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not a trivial task (e.g. you cannot load all the variants into XLS
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spreadsheet). SnpSift helps to perform this VCF file manipulation and
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filtering required at this stage in data processing pipelines.
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If you are using SnpEff or SnpSift, please cite:
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A program for annotating and predicting the effects of single
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nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila
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melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang
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le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin).
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2012 Apr-Jun;6(2):80-92. PMID: 22728672
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23
academic/snpEff/References
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academic/snpEff/References
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f you are using SnpEff or SnpSift, please cite our work.
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Citing SnpEff:
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"A program for annotating and predicting the effects of single
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nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila
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melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang
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le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin).
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2012 Apr-Jun;6(2):80-92. PMID: 22728672
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You can find the paper here:
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http://snpeff.sourceforge.net/SnpEff_paper.pdf
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BibTex entry:
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@article{cingolani2012program,
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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},
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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.},
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journal={Fly},
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volume={6},
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number={2},
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pages={80-92},
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year={2012}
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}
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19
academic/snpEff/slack-desc
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academic/snpEff/slack-desc
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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snpEff: snpEff (Genetic variant annotation and effect prediction toolbox)
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snpEff:
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snpEff: SnpEff is a variant annotation and effect prediction tool. It
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snpEff: annotates and predicts the effects of variants on genes (such
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snpEff: as amino acid changes).
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snpEff:
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snpEff: Home: http://snpeff.sourceforge.net/
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snpEff: References: /usr/doc/snpEff-4.1b/References
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snpEff:
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snpEff:
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snpEff:
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74
academic/snpEff/snpEff.SlackBuild
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academic/snpEff/snpEff.SlackBuild
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#!/bin/sh
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# Slackware build script for snpEff
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# Copyright 2015 Petar Petrov petar.petrov@student.oulu.fi
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=snpEff
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VERSION=${VERSION:-4.1b}
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SRCVER=${SRCVER:-v4_1b}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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ARCH=noarch
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM
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unzip $CWD/${PRGNAM}_${SRCVER}_core.zip
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cd $PRGNAM
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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mkdir -p $PKG/usr/share/java/$PRGNAM
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cp -a examples galaxy scripts $PRGNAM.config $PRGNAM.jar SnpSift.jar \
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$PKG/usr/share/java/$PRGNAM
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mkdir -p $PKG/usr/bin
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cd $PKG/usr/bin
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ln -s ../share/java/$PRGNAM/snpEff.jar
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ln -s ../share/java/$PRGNAM/SnpSift.jar
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cd -
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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10
academic/snpEff/snpEff.info
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academic/snpEff/snpEff.info
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PRGNAM="snpEff"
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VERSION="4.1b"
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HOMEPAGE="http://snpeff.sourceforge.net/"
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DOWNLOAD="http://sourceforge.net/projects/snpeff/files/snpEff_v4_1b_core.zip"
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MD5SUM="60ba0104e63aef0b8ddbd62610af328a"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="jdk"
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MAINTAINER="Petar Petrov"
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EMAIL="petar.petrov@student.oulu.fi"
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