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academic/megacc: Removed (see megax).
The new megax SlackBuild includes megacc. Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
This commit is contained in:
Petar Petrov
David Spencer
parent
678b09e63c
commit
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MEGA: Molecular Evolutionary Genetics Analysis
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Sophisticated and user-friendly software suite for analyzing DNA and
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protein sequence data from species and populations.
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MEGA-CC is the command-line version of MEGA that implements its core
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analysis functions and is useful for iterative and automated execution.
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There are two executables: megacc and megaproto. Start with megaproto
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which is used to create a MEGA Analysis Options (.mao) file that
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specifies the analysis to run as well as relevant options. Then you call
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megacc from a command shell and pass the .mao filename and input data
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filenames as parameters. For example:
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megacc -a myMaoFile.mao -d mySequenceAlignment.fas -o myOutput
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To get started, checkout MEGA7-CC-User-Manual.pdf, found in the
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documentation folder of the installed package.
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This SlackBuild just repackages the binaries provided from upstream.
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There are no 32bit executables.
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NOTE! IMPORTANT!
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MEGA-CC is not free software. Your use of MEGA-CC is subject to the
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licence agreement at:
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http://www.megasoftware.net/show_eua
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SlackBuilds.org thanks Prof. Kumar for permission to use the direct
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download URL.
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Citing:
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MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger
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datasets (Kumar, Stecher, and Tamura 2015).
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http://www.megasoftware.net/citations
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MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger
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datasets
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Kumar S, Stecher G, and Tamura K (2016)
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Molecular Biology and Evolution 33:1870-1874
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MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
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Tamura K, Stecher G, Peterson D, Filipski A, and Kumar S (2013)
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Molecular Biology and Evolution 30:2725-2729
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MEGA-CC: Computing Core of Molecular Evolutionary Genetics Analysis
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Program for Automated and Iterative Data Analysis
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Kumar S, Stecher G, Peterson D, and Tamura K (2012)
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Bioinformatics 28:2685-2686
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MEGA5: Molecular Evolutionary Genetic Analysis using Maximum Likelihood,
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Evolutionary Distance, and Maximum Parsimony Methods
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Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011)
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Molecular Biology and Evolution 28:2731-2739
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MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version
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4.0
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Tamura K, Dudley J, Nei M and Kumar S (2007)
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Molecular Biology and Evolution 24:1596-1599
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if [ -x /usr/bin/update-desktop-database ]; then
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/usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
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fi
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#!/bin/sh
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# Slackware build script for megacc
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# Copyright 2017 Petar Petrov slackalaxy@gmail.com
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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=megacc
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VERSION=${VERSION:-7.0.26_1}
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TARVER=7.0.26-1
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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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=${OUTPUT:-/tmp}
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set -e
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# Stop if processor architecture is not supported
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if [ "$ARCH" != "x86_64" ]; then
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printf "\n\n$ARCH is not supported... \n"
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exit 1
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fi
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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 $PRGNAM-$VERSION
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mkdir $PRGNAM-$VERSION
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cd $PRGNAM-$VERSION
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tar xvf $CWD/$PRGNAM-${TARVER}.${ARCH}.tar.gz
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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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# Install the two binaries
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install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM
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install -D -m755 megaproto $PKG/usr/bin/megaproto
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# Place the man page in its proper location
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install -D -m644 $PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1
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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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find $PKG/usr/man -type f -exec gzip -9 {} \;
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for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
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# Include examples
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mkdir -p $PKG/usr/share/$PRGNAM
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cp -a Examples/* $PKG/usr/share/$PRGNAM
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# Menu entry for Megaproto
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mkdir -p $PKG/usr/share/{applications,pixmaps}
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cp $CWD/megaproto.desktop $PKG/usr/share/applications
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cp $CWD/megaproto.png $PKG/usr/share/pixmaps
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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Mega7.chm MEGA7-CC-User-Manual.pdf readme.txt usageAgreement.txt \
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$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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cat $CWD/doinst.sh > $PKG/install/doinst.sh
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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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PRGNAM="megacc"
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VERSION="7.0.26_1"
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HOMEPAGE="http://www.megasoftware.net/"
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DOWNLOAD="UNSUPPORTED"
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MD5SUM=""
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DOWNLOAD_x86_64="http://www.megasoftware.net/releases/megacc-7.0.26-1.x86_64.tar.gz"
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MD5SUM_x86_64="29638dd06536b84dd2c7b8fb19541c9e"
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REQUIRES=""
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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[Desktop Entry]
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Categories=Education;
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Comment=Molecular evolutionary genetics analysis
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Exec=megaproto
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Icon=megaproto
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Name=MEGA Proto
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StartupNotify=false
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Type=Application
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Binary file not shown.
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Before Width: | Height: | Size: 1.4 KiB |
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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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megacc: megacc (Molecular Evolutionary Genetics Analysis)
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megacc:
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megacc: Sophisticated and user-friendly software suite for analyzing DNA
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megacc: and protein sequence data from species and populations.
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megacc:
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megacc: Home: http://www.megasoftware.net/
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megacc: Citations: http://www.megasoftware.net/citations
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megacc:
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megacc:
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megacc:
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megacc:
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