From 3ef60ddb51c13b21f142bc180e7b621f6b0b5a9e Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Wed, 1 Oct 2014 07:43:31 +0700 Subject: academic/archeopteryx: Added (phylogenetic trees analyzer). Signed-off-by: Willy Sudiarto Raharjo --- academic/archeopteryx/README | 11 +++++ academic/archeopteryx/References | 4 ++ academic/archeopteryx/archeopteryx.SlackBuild | 60 ++++++++++++++++++++++++++ academic/archeopteryx/archeopteryx.desktop | 7 +++ academic/archeopteryx/archeopteryx.info | 10 +++++ academic/archeopteryx/archeopteryx.png | Bin 0 -> 39248 bytes academic/archeopteryx/doinst.sh | 3 ++ academic/archeopteryx/slack-desc | 19 ++++++++ 8 files changed, 114 insertions(+) create mode 100644 academic/archeopteryx/README create mode 100644 academic/archeopteryx/References create mode 100644 academic/archeopteryx/archeopteryx.SlackBuild create mode 100644 academic/archeopteryx/archeopteryx.desktop create mode 100644 academic/archeopteryx/archeopteryx.info create mode 100644 academic/archeopteryx/archeopteryx.png create mode 100644 academic/archeopteryx/doinst.sh create mode 100644 academic/archeopteryx/slack-desc (limited to 'academic') diff --git a/academic/archeopteryx/README b/academic/archeopteryx/README new file mode 100644 index 0000000000..f5940b6f7f --- /dev/null +++ b/academic/archeopteryx/README @@ -0,0 +1,11 @@ +Archaeopteryx: visualise, analyse and edit phylogenetic trees + +Archaeopteryx is a software tool for the visualization, analysis, and +editing of potentially large and highly annotated phylogenetic trees. +Archaeopteryx (the successor to ATV) is entirely written in the Java +programming language and is based on the forester libraries. + +Please cite: +Han M.V. and Zmasek C.M. (2009) +phyloXML: XML for evolutionary biology and comparative genomics +BMC Bioinformatics, 10:356. diff --git a/academic/archeopteryx/References b/academic/archeopteryx/References new file mode 100644 index 0000000000..bec0a4ddb1 --- /dev/null +++ b/academic/archeopteryx/References @@ -0,0 +1,4 @@ +Please cite: +Han M.V. and Zmasek C.M. (2009) +phyloXML: XML for evolutionary biology and comparative genomics +BMC Bioinformatics, 10:356. diff --git a/academic/archeopteryx/archeopteryx.SlackBuild b/academic/archeopteryx/archeopteryx.SlackBuild new file mode 100644 index 0000000000..6f8327f389 --- /dev/null +++ b/academic/archeopteryx/archeopteryx.SlackBuild @@ -0,0 +1,60 @@ +#!/bin/sh + +# Slackware build script for archeopteryx + +# Copyright 2014 Petar Petrov petar.petrov@student.oulu.fi +# 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=archeopteryx +VERSION=${VERSION:-0.9899_beta} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=forester +SRCVER=1037 +ARCH=noarch + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP + +install -D -m755 $CWD/${SRCNAM}_${SRCVER}.jar $PKG/usr/bin/$PRGNAM.jar + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +# I did not find an icon, so I quickly modified some picture of an archeopteryx... +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications +cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps + +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/archeopteryx/archeopteryx.desktop b/academic/archeopteryx/archeopteryx.desktop new file mode 100644 index 0000000000..8387b60fd9 --- /dev/null +++ b/academic/archeopteryx/archeopteryx.desktop @@ -0,0 +1,7 @@ +[Desktop Entry] +Categories=Education; +Exec=java -Xmx2048m -jar /usr/bin/archeopteryx.jar +Icon=archeopteryx.png +Name=Archeopteryx +StartupNotify=false +Type=Application diff --git a/academic/archeopteryx/archeopteryx.info b/academic/archeopteryx/archeopteryx.info new file mode 100644 index 0000000000..3b8f7310b9 --- /dev/null +++ b/academic/archeopteryx/archeopteryx.info @@ -0,0 +1,10 @@ +PRGNAM="archeopteryx" +VERSION="0.9899_beta" +HOMEPAGE="https://sites.google.com/site/cmzmasek/home/software/archaeopteryx" +DOWNLOAD="https://googledrive.com/host/0BxMokdxOh-JRM1d2azFoRnF3bGM/download/forester_1037.jar" +MD5SUM="84fdaf7ab00b4d1be16ce0ace2289e1a" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="jdk" +MAINTAINER="Petar Petrov" +EMAIL="petar.petrov@student.oulu.fi" diff --git a/academic/archeopteryx/archeopteryx.png b/academic/archeopteryx/archeopteryx.png new file mode 100644 index 0000000000..5663c1b87e Binary files /dev/null and b/academic/archeopteryx/archeopteryx.png differ diff --git a/academic/archeopteryx/doinst.sh b/academic/archeopteryx/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/archeopteryx/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/archeopteryx/slack-desc b/academic/archeopteryx/slack-desc new file mode 100644 index 0000000000..1bd01361d1 --- /dev/null +++ b/academic/archeopteryx/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------------------------------------------------------| +archeopteryx: archeopteryx (Visualise, analyse and edit phylogenetic trees) +archeopteryx: +archeopteryx: Archaeopteryx is a software tool for the visualization, analysis, +archeopteryx: and editing of potentially large and highly annotated phylogenetic +archeopteryx: trees. +archeopteryx: +archeopteryx: +archeopteryx: +archeopteryx: +archeopteryx: +archeopteryx: -- cgit v1.2.3