From 30bc07bbf06b29cc0d5e0fc08928ab4851bdd3d1 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Wed, 19 Apr 2017 11:01:35 +0100 Subject: academic/megacc: Added (Molecular Evolutionary Genetics Analysis). Signed-off-by: David Spencer --- academic/megacc/README | 37 ++++++++++++++ academic/megacc/References | 25 ++++++++++ academic/megacc/doinst.sh | 3 ++ academic/megacc/megacc.SlackBuild | 100 ++++++++++++++++++++++++++++++++++++++ academic/megacc/megacc.info | 10 ++++ academic/megacc/megaproto.desktop | 8 +++ academic/megacc/megaproto.png | Bin 0 -> 1470 bytes academic/megacc/slack-desc | 19 ++++++++ 8 files changed, 202 insertions(+) create mode 100644 academic/megacc/README create mode 100644 academic/megacc/References create mode 100644 academic/megacc/doinst.sh create mode 100644 academic/megacc/megacc.SlackBuild create mode 100644 academic/megacc/megacc.info create mode 100644 academic/megacc/megaproto.desktop create mode 100644 academic/megacc/megaproto.png create mode 100644 academic/megacc/slack-desc (limited to 'academic') diff --git a/academic/megacc/README b/academic/megacc/README new file mode 100644 index 0000000000..ccb0a7bdf6 --- /dev/null +++ b/academic/megacc/README @@ -0,0 +1,37 @@ +MEGA: Molecular Evolutionary Genetics Analysis + +Sophisticated and user-friendly software suite for analyzing DNA and +protein sequence data from species and populations. + +MEGA-CC is the command-line version of MEGA that implements its core +analysis functions and is useful for iterative and automated execution. +There are two executables: megacc and megaproto. Start with megaproto +which is used to create a MEGA Analysis Options (.mao) file that +specifies the analysis to run as well as relevant options. Then you call +megacc from a command shell and pass the .mao filename and input data +filenames as parameters. For example: + +megacc -a myMaoFile.mao -d mySequenceAlignment.fas -o myOutput + +To get started, checkout MEGA7-CC-User-Manual.pdf, found in the +documentation folder of the installed package. + +This SlackBuild just repackages the binaries provided from upstream. +There are no 32bit executables. + + +NOTE! IMPORTANT! + +MEGA-CC is not free software. Your use of MEGA-CC is subject to the +licence agreement at: + + http://www.megasoftware.net/show_eua + +SlackBuilds.org thanks Prof. Kumar for permission to use the direct +download URL. + + +Citing: + +MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger +datasets (Kumar, Stecher, and Tamura 2015). diff --git a/academic/megacc/References b/academic/megacc/References new file mode 100644 index 0000000000..c05107d41d --- /dev/null +++ b/academic/megacc/References @@ -0,0 +1,25 @@ +http://www.megasoftware.net/citations + +MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger +datasets +Kumar S, Stecher G, and Tamura K (2016) +Molecular Biology and Evolution 33:1870-1874 + +MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 +Tamura K, Stecher G, Peterson D, Filipski A, and Kumar S (2013) +Molecular Biology and Evolution 30:2725-2729 + +MEGA-CC: Computing Core of Molecular Evolutionary Genetics Analysis +Program for Automated and Iterative Data Analysis +Kumar S, Stecher G, Peterson D, and Tamura K (2012) +Bioinformatics 28:2685-2686 + +MEGA5: Molecular Evolutionary Genetic Analysis using Maximum Likelihood, +Evolutionary Distance, and Maximum Parsimony Methods +Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011) +Molecular Biology and Evolution 28:2731-2739 + +MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version +4.0 +Tamura K, Dudley J, Nei M and Kumar S (2007) +Molecular Biology and Evolution 24:1596-1599 diff --git a/academic/megacc/doinst.sh b/academic/megacc/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/megacc/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/megacc/megacc.SlackBuild b/academic/megacc/megacc.SlackBuild new file mode 100644 index 0000000000..a9e90674bf --- /dev/null +++ b/academic/megacc/megacc.SlackBuild @@ -0,0 +1,100 @@ +#!/bin/sh + +# Slackware build script for megacc + +# Copyright 2017 Petar Petrov slackalaxy@gmail.com +# 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=megacc +VERSION=${VERSION:-7.0.25_1} +TARVER=7.0.25-1 +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +# Stop if processor architecture is not supported +if [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-${TARVER}.${ARCH}.tar.gz +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 {} \; + +# Install the two binaries +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM +install -D -m755 megaproto $PKG/usr/bin/megaproto + +# Place the man page in its proper location +install -D -m644 $PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1 + +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 + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +# Include examples +mkdir -p $PKG/usr/share/$PRGNAM +cp -a Examples/* $PKG/usr/share/$PRGNAM + +# Menu entry for Megaproto +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/megaproto.desktop $PKG/usr/share/applications +cp $CWD/megaproto.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + Mega7.chm MEGA7-CC-User-Manual.pdf readme.txt usageAgreement.txt \ + $PKG/usr/doc/$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 +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/megacc/megacc.info b/academic/megacc/megacc.info new file mode 100644 index 0000000000..8c5bd01d90 --- /dev/null +++ b/academic/megacc/megacc.info @@ -0,0 +1,10 @@ +PRGNAM="megacc" +VERSION="7.0.25_1" +HOMEPAGE="http://www.megasoftware.net/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="http://www.megasoftware.net/releases/megacc-7.0.25-1.x86_64.tar.gz" +MD5SUM_x86_64="42cff0d3c1e0dbf664c8dc75d17fa39e" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/megacc/megaproto.desktop b/academic/megacc/megaproto.desktop new file mode 100644 index 0000000000..4ef7569ee1 --- /dev/null +++ b/academic/megacc/megaproto.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Categories=Education; +Comment=Molecular evolutionary genetics analysis +Exec=megaproto +Icon=megaproto +Name=MEGA Proto +StartupNotify=false +Type=Application diff --git a/academic/megacc/megaproto.png b/academic/megacc/megaproto.png new file mode 100644 index 0000000000..92fec00c7b Binary files /dev/null and b/academic/megacc/megaproto.png differ diff --git a/academic/megacc/slack-desc b/academic/megacc/slack-desc new file mode 100644 index 0000000000..03b416b6fc --- /dev/null +++ b/academic/megacc/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------------------------------------------------------| +megacc: megacc (Molecular Evolutionary Genetics Analysis) +megacc: +megacc: Sophisticated and user-friendly software suite for analyzing DNA +megacc: and protein sequence data from species and populations. +megacc: +megacc: Home: http://www.megasoftware.net/ +megacc: Citations: http://www.megasoftware.net/citations +megacc: +megacc: +megacc: +megacc: -- cgit v1.2.3