From 678b09e63cc6588808f18215c870ff688038843c Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Fri, 13 Jul 2018 23:14:52 +0100 Subject: academic/megax: Added (Molecular Evolutionary Genetics Analysis). Signed-off-by: David Spencer --- academic/megax/README | 47 +++++++++++++++++ academic/megax/References | 25 +++++++++ academic/megax/doinst.sh | 3 ++ academic/megax/megax.SlackBuild | 110 ++++++++++++++++++++++++++++++++++++++++ academic/megax/megax.desktop | 9 ++++ academic/megax/megax.info | 10 ++++ academic/megax/slack-desc | 19 +++++++ 7 files changed, 223 insertions(+) create mode 100644 academic/megax/README create mode 100644 academic/megax/References create mode 100644 academic/megax/doinst.sh create mode 100644 academic/megax/megax.SlackBuild create mode 100644 academic/megax/megax.desktop create mode 100644 academic/megax/megax.info create mode 100644 academic/megax/slack-desc (limited to 'academic') diff --git a/academic/megax/README b/academic/megax/README new file mode 100644 index 0000000000..8cf4eee34c --- /dev/null +++ b/academic/megax/README @@ -0,0 +1,47 @@ +MEGA: Molecular Evolutionary Genetics Analysis + +Sophisticated and user-friendly software suite for analyzing DNA and +protein sequence data from species and populations. MEGA can be used +with either a graphical user interface, useful for visual exploration +of data and results or a command-line interface (useful for batch or +scripted execution). + +MEGA X +MEGA X is the GUI graphical user interface of MEGA and can be run in +one of two modes. The first mode is the "Analyze mode" in which all +GUI tools in MEGA are enabled and visual results explorers are +available for tasks such as editing sequence alignments and viewing +phylogenies. This is the mode that most MEGA users are familiar with. +The second mode is the Prototype mode which is used solely for +generating MEGA Analysis Options (.mao) files that specify analysis +settings when using MEGA from a command shell (megacc). In the MEGA +main form, click the Prototype button and then specify the type of +input data that will be used for analysis. + +MEGA CC +The command-line version of MEGA is 'megacc', that implements its core +analysis functions and is useful for iterative and automated execution. +The megacc command requires several options, including the path to a +.mao file and paths to input data file(s) to be analyzed. For example: + +$ megacc -a myMaoFile.mao -d mySequenceAlignment.fas -o myOutput + +Note 1. +Upon start, MEGA X will create an examples folder with the same name +in your user's home. This is a good place to start if you are not +familiar with MEGA. + +Note 2. +This SlackBuild just repackages the binaries for Debian, provided from +upstream. The RedHat packages, currently, do not have 32bit version. + +Note 3. IMPORTANT! +SlackBuilds.org thanks Prof. Kumar for permission to use the direct +download URL. MEGA is not free software. Your use is subject to the +licence agreement at: + +http://www.megasoftware.net/show_eua + +Citing: +MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger +datasets (Kumar, Stecher, and Tamura 2015). diff --git a/academic/megax/References b/academic/megax/References new file mode 100644 index 0000000000..c05107d41d --- /dev/null +++ b/academic/megax/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/megax/doinst.sh b/academic/megax/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/megax/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/megax/megax.SlackBuild b/academic/megax/megax.SlackBuild new file mode 100644 index 0000000000..b33801c213 --- /dev/null +++ b/academic/megax/megax.SlackBuild @@ -0,0 +1,110 @@ +#!/bin/sh + +# Slackware build script for megax +# This takes the place of "megacc" in 2018, as it includes also the GUI +# of the program (megax) in addition to megacc. + +# Copyright 2017-2018 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=megax +VERSION=${VERSION:-10.0.4_1} +DEBVER=10.0.4-1 +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i386 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i386" ] || [ "$ARCH" = "i486" ] || [ "$ARCH" = "i586" ] || [ "$ARCH" = "i686" ]; then + LIBDIRSUFFIX="" + DEBARCH="i386" +elif [ "$ARCH" = "x86_64" ]; then + LIBDIRSUFFIX="64" + DEBARCH="amd64" +else + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +ar p $CWD/${PRGNAM}_${DEBVER}_${DEBARCH}.deb data.tar.xz | tar xJv +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 {} \; + +# Fix path in runmega.sh for x86_64 +sed -i "s|/usr/lib/megax|/usr/lib${LIBDIRSUFFIX}/megax|g" usr/lib/$PRGNAM/runmega.sh + +# Place things in /usr/lib and just create symlinks later. +# This is what Debian's and RedHat's packages do. +mkdir -p $PKG/usr/lib${LIBDIRSUFFIX} +cp -a usr/lib/$PRGNAM $PKG/usr/lib${LIBDIRSUFFIX} + +# Copy man pages to their proper place. +cp -a usr/local/share/man $PKG/usr + +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +ln -s ../lib${LIBDIRSUFFIX}/$PRGNAM/megacc +ln -s ../lib${LIBDIRSUFFIX}/$PRGNAM/runmega.sh megax +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 + +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 + +# Menu entry for MEGA X, use our .desktop file +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications +cp usr/share/pixmaps/mega.png $PKG/usr/share/pixmaps/megax.png + +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 +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/megax/megax.desktop b/academic/megax/megax.desktop new file mode 100644 index 0000000000..336d4eb395 --- /dev/null +++ b/academic/megax/megax.desktop @@ -0,0 +1,9 @@ +[Desktop Entry] +Categories=Education; +Comment=Molecular evolutionary genetics analysis +Exec=megax +Icon=megax +Name=MEGA X +StartupNotify=false +Terminal=false +Type=Application diff --git a/academic/megax/megax.info b/academic/megax/megax.info new file mode 100644 index 0000000000..f5d2e5de27 --- /dev/null +++ b/academic/megax/megax.info @@ -0,0 +1,10 @@ +PRGNAM="megax" +VERSION="10.0.4_1" +HOMEPAGE="http://www.megasoftware.net/" +DOWNLOAD="https://www.megasoftware.net/releases/megax_10.0.4-1_i386.deb" +MD5SUM="0c5b9b6ea6521000a1f6827422143448" +DOWNLOAD_x86_64="https://www.megasoftware.net/releases/megax_10.0.4-1_amd64.deb" +MD5SUM_x86_64="ca19228cfcee9d6603219e8ab3153141" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/megax/slack-desc b/academic/megax/slack-desc new file mode 100644 index 0000000000..ba4b953325 --- /dev/null +++ b/academic/megax/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------------------------------------------------------| +megax: megax (Molecular Evolutionary Genetics Analysis) +megax: +megax: Sophisticated and user-friendly software suite for analyzing DNA +megax: and protein sequence data from species and populations. MEGA can +megax: be used with either a graphical user interface, useful for visual +megax: exploration of data and results or a command-line interface +megax: (useful for batch or scripted execution). +megax: +megax: Home: https://www.megasoftware.net/ +megax: Publications: https://www.megasoftware.net/citations +megax: Documentation: https://www.megasoftware.net/web_help_10/index.htm -- cgit v1.2.3