academic/megax: Added (Molecular Evolutionary Genetics Analysis).

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

7 files changed, 223 insertions, 0 deletions

diff --git a/academic/megax/README b/academic/megax/README
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+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
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+++ 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 000000000000..5fb28930db0b
--- /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 000000000000..b33801c213c9
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+++ 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
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+++ b/academic/megax/megax.desktop
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+[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 000000000000..f5d2e5de27cd
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+++ 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
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index 000000000000..ba4b9533250b
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+++ 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