academic/snpEff: Added (Genes toolbox).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

5 files changed, 154 insertions, 0 deletions

diff --git a/academic/snpEff/README b/academic/snpEff/README
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+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
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+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
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+# 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
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index 0000000000000..6f0e9e41cd578
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+++ b/academic/snpEff/snpEff.SlackBuild
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+#!/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
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index 0000000000000..92804c89ae0fc
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+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"