From 552e8af4324cff571dd6ef7b2bc60d3e85082d23 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Tue, 19 Jun 2018 23:35:56 +0100 Subject: academic/TreeGraph: Added (A feature rich phylogenetic tree editor). Signed-off-by: David Spencer --- academic/TreeGraph/README | 41 ++++++++++++++++ academic/TreeGraph/TreeGraph | 4 ++ academic/TreeGraph/TreeGraph.SlackBuild | 80 ++++++++++++++++++++++++++++++++ academic/TreeGraph/TreeGraph.desktop | 8 ++++ academic/TreeGraph/TreeGraph.info | 10 ++++ academic/TreeGraph/TreeGraph.png | Bin 0 -> 10235 bytes academic/TreeGraph/doinst.sh | 3 ++ academic/TreeGraph/slack-desc | 19 ++++++++ 8 files changed, 165 insertions(+) create mode 100644 academic/TreeGraph/README create mode 100644 academic/TreeGraph/TreeGraph create mode 100644 academic/TreeGraph/TreeGraph.SlackBuild create mode 100644 academic/TreeGraph/TreeGraph.desktop create mode 100644 academic/TreeGraph/TreeGraph.info create mode 100644 academic/TreeGraph/TreeGraph.png create mode 100644 academic/TreeGraph/doinst.sh create mode 100644 academic/TreeGraph/slack-desc (limited to 'academic/TreeGraph') diff --git a/academic/TreeGraph/README b/academic/TreeGraph/README new file mode 100644 index 0000000000..9377b9be73 --- /dev/null +++ b/academic/TreeGraph/README @@ -0,0 +1,41 @@ +TreeGraph (2): A feature rich and easy to use phylogenetic tree editor + +TreeGraph (2) is a is graphical editor for phylogenetic trees, which +allows to apply various of graphical formats and edit operations and +supports several (visible or invisible) annotations attached to nodes +or branches. Data can be imported from many tree formats, tables and +BayesTraits output. + +A key feature is the interactive comparison and combination of +alternative topologies from different analyses. + +Key features +- Read trees in Newick, Nexus format (including annotations in hot + comments), NeXML or PhyloXML +- Import annotations from text files or combine information from + different phylogenetic analyses +- An unlimited number of numerical or textual annotations on every + branch +- Export trees to various vector and (anti-aliased) pixel graphic + formats (e.g. PDF, SVG, EMF or PNG) +- Many global and element specific formats like line width or color + and text formats +- Versatile editing and formatting options, such as automatically + setting branch widths or colors according to the value of any + attached data +- Editing operations like rerooting, ladderizing or moving and + collapsing nodes or copying or manually creating whole clades +- Generate commands and import data for ancestral state reconstruction + +Citation +TreeGraph 2 has been published in BMC Bioinformatics: +Stöver BC, Müller KF: TreeGraph 2: Combining and visualizing evidence +from different phylogenetic analyses. BMC Bioinformatics 2010, 11:7 +DOI: 10.1186/1471-2105-11-7 + + +IMPORTANT NOTE ABOUT THE DOWNLOAD + +If you have trouble with the download, please use a browser to visit +the TreeGraph download page at http://treegraph.bioinfweb.info/Download +and click the download link. diff --git a/academic/TreeGraph/TreeGraph b/academic/TreeGraph/TreeGraph new file mode 100644 index 0000000000..aee6d91990 --- /dev/null +++ b/academic/TreeGraph/TreeGraph @@ -0,0 +1,4 @@ +#!/bin/sh + +cd /usr/share/java/TreeGraph +java -jar TreeGraph.jar & diff --git a/academic/TreeGraph/TreeGraph.SlackBuild b/academic/TreeGraph/TreeGraph.SlackBuild new file mode 100644 index 0000000000..a3f304b739 --- /dev/null +++ b/academic/TreeGraph/TreeGraph.SlackBuild @@ -0,0 +1,80 @@ +#!/bin/sh + +# Slackware build script for TreeGraph + +# Copyright 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=TreeGraph +VERSION=${VERSION:-2.14.0_771_beta} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +ZIPVER=2.14.0-771_beta +ARCH=noarch + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir -p $PRGNAM-$VERSION +cd $PRGNAM-$VERSION + +# Use "bsdtar" instead of "unzip". The latter has some bug which +# prevented the script from running past the unzipping step. Or maybe +# I did sth wrong here... +bsdtar -xf $CWD/${PRGNAM}_${ZIPVER}.zip +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 {} \; + +# There are a bunch of LICENSE-* txt files, however leave them there, +# otherwise the program will fail to start. I tried moving them to +# $PKG/usr/doc/$PRGNAM-$VERSION and had an error message upon start. +mkdir -p $PKG/usr/share/java/$PRGNAM/lib/{batik,errorReporter} +cp -a icons lib $PRGNAM.jar $PKG/usr/share/java/$PRGNAM + +# Install our simple wrapper +install -D -m755 $CWD/$PRGNAM $PKG/usr/bin/$PRGNAM + +# Include our own icon and desktop file +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 $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +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/TreeGraph/TreeGraph.desktop b/academic/TreeGraph/TreeGraph.desktop new file mode 100644 index 0000000000..51e4d0a549 --- /dev/null +++ b/academic/TreeGraph/TreeGraph.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Categories=Education; +Comment=A feature rich and easy to use phylogenetic tree editor +Exec=TreeGraph +Icon=TreeGraph +Name=TreeGraph 2 +StartupNotify=false +Type=Application diff --git a/academic/TreeGraph/TreeGraph.info b/academic/TreeGraph/TreeGraph.info new file mode 100644 index 0000000000..04673ad615 --- /dev/null +++ b/academic/TreeGraph/TreeGraph.info @@ -0,0 +1,10 @@ +PRGNAM="TreeGraph" +VERSION="2.14.0_771_beta" +HOMEPAGE="http://treegraph.bioinfweb.info/" +DOWNLOAD="http://treegraph.bioinfweb.info/Download/Complete/TreeGraph_2.14.0-771_beta.zip" +MD5SUM="78dbfd08f946bb46622314457a25a78e" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="jdk" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/TreeGraph/TreeGraph.png b/academic/TreeGraph/TreeGraph.png new file mode 100644 index 0000000000..25b57a6add Binary files /dev/null and b/academic/TreeGraph/TreeGraph.png differ diff --git a/academic/TreeGraph/doinst.sh b/academic/TreeGraph/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/TreeGraph/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/TreeGraph/slack-desc b/academic/TreeGraph/slack-desc new file mode 100644 index 0000000000..c4af759a8e --- /dev/null +++ b/academic/TreeGraph/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------------------------------------------------------| +TreeGraph: TreeGraph (A feature rich phylogenetic tree editor) +TreeGraph: +TreeGraph: TreeGraph 2 is a is graphical editor for phylogenetic trees, +TreeGraph: which allows to apply various of graphical formats and edit +TreeGraph: operations and supports several annotations attached to nodes +TreeGraph: or branches. Data can be imported from many tree formats, +TreeGraph: tables and BayesTraits output. A key feature is the interactive +TreeGraph: comparison and combination of alternative topologies from +TreeGraph: different analyses. +TreeGraph: +TreeGraph: http://treegraph.bioinfweb.info/ -- cgit v1.2.3