From ee0cf21841b2a71ce334159c3e275475d7a75bb8 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Fri, 13 Jul 2018 23:17:29 +0100 Subject: academic/megacc: Removed (see megax). The new megax SlackBuild includes megacc. 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 1470 -> 0 bytes academic/megacc/slack-desc | 19 -------- 8 files changed, 202 deletions(-) delete mode 100644 academic/megacc/README delete mode 100644 academic/megacc/References delete mode 100644 academic/megacc/doinst.sh delete mode 100644 academic/megacc/megacc.SlackBuild delete mode 100644 academic/megacc/megacc.info delete mode 100644 academic/megacc/megaproto.desktop delete mode 100644 academic/megacc/megaproto.png delete mode 100644 academic/megacc/slack-desc diff --git a/academic/megacc/README b/academic/megacc/README deleted file mode 100644 index ccb0a7bdf6..0000000000 --- a/academic/megacc/README +++ /dev/null @@ -1,37 +0,0 @@ -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 deleted file mode 100644 index c05107d41d..0000000000 --- a/academic/megacc/References +++ /dev/null @@ -1,25 +0,0 @@ -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 deleted file mode 100644 index 5fb28930db..0000000000 --- a/academic/megacc/doinst.sh +++ /dev/null @@ -1,3 +0,0 @@ -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 deleted file mode 100644 index c7d2689033..0000000000 --- a/academic/megacc/megacc.SlackBuild +++ /dev/null @@ -1,100 +0,0 @@ -#!/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=${VERSION:-7.0.26_1} -TARVER=7.0.26-1 -BUILD=${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 deleted file mode 100644 index 6d18875735..0000000000 --- a/academic/megacc/megacc.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="megacc" -VERSION="7.0.26_1" -HOMEPAGE="http://www.megasoftware.net/" -DOWNLOAD="UNSUPPORTED" -MD5SUM="" -DOWNLOAD_x86_64="http://www.megasoftware.net/releases/megacc-7.0.26-1.x86_64.tar.gz" -MD5SUM_x86_64="29638dd06536b84dd2c7b8fb19541c9e" -REQUIRES="" -MAINTAINER="Petar Petrov" -EMAIL="slackalaxy@gmail.com" diff --git a/academic/megacc/megaproto.desktop b/academic/megacc/megaproto.desktop deleted file mode 100644 index 4ef7569ee1..0000000000 --- a/academic/megacc/megaproto.desktop +++ /dev/null @@ -1,8 +0,0 @@ -[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 deleted file mode 100644 index 92fec00c7b..0000000000 Binary files a/academic/megacc/megaproto.png and /dev/null differ diff --git a/academic/megacc/slack-desc b/academic/megacc/slack-desc deleted file mode 100644 index 03b416b6fc..0000000000 --- a/academic/megacc/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# 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