From c5710a1ef12ae9417e5f08a752df336c406299a7 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Tue, 10 Jul 2018 10:06:17 +0100 Subject: academic/treeviewx: Added (Program to display phylogenetic trees). Renamed from academic/treeview, to avoid confusion with a different package also named Treeview. Signed-off-by: David Spencer --- academic/treeviewx/README | 23 +++++++ academic/treeviewx/References | 3 + academic/treeviewx/cstring.patch | 71 ++++++++++++++++++++ academic/treeviewx/doinst.sh | 3 + academic/treeviewx/slack-desc | 19 ++++++ academic/treeviewx/treeviewx.SlackBuild | 113 ++++++++++++++++++++++++++++++++ academic/treeviewx/treeviewx.desktop | 8 +++ academic/treeviewx/treeviewx.info | 10 +++ academic/treeviewx/treeviewx.png | Bin 0 -> 17326 bytes 9 files changed, 250 insertions(+) create mode 100644 academic/treeviewx/README create mode 100644 academic/treeviewx/References create mode 100644 academic/treeviewx/cstring.patch create mode 100644 academic/treeviewx/doinst.sh create mode 100644 academic/treeviewx/slack-desc create mode 100644 academic/treeviewx/treeviewx.SlackBuild create mode 100644 academic/treeviewx/treeviewx.desktop create mode 100644 academic/treeviewx/treeviewx.info create mode 100644 academic/treeviewx/treeviewx.png (limited to 'academic/treeviewx') diff --git a/academic/treeviewx/README b/academic/treeviewx/README new file mode 100644 index 0000000000..9e1dcb3422 --- /dev/null +++ b/academic/treeviewx/README @@ -0,0 +1,23 @@ +Rod Page's TreeView X is a simple program for displaying phylogenies. +Some of its features include: + +- reads many different tree file formats (including NEXUS, PHYLIP, + Hennig86, NONA, MEGA, and ClustalW/X) +- supports standard the TrueType and Postscript fonts +- supports native graphics file format for copying pictures into + other applications, and for saving graphics files +- print preview +- can print multiple trees per page and/or one tree over more than + one page +- has drag-and-drop facility for easy opening of files +- Web-based online help +- tree editor + +Note! +This program is different from Michael Eisen's TreeView for matrix- +like display of expression data. + +For details and citation: +Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic +trees on personal computers. Computer Applications in the Biosciences +12: 357-358. diff --git a/academic/treeviewx/References b/academic/treeviewx/References new file mode 100644 index 0000000000..4d53820121 --- /dev/null +++ b/academic/treeviewx/References @@ -0,0 +1,3 @@ +Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic +trees on personal computers. Computer Applications in the Biosciences +12: 357-358 diff --git a/academic/treeviewx/cstring.patch b/academic/treeviewx/cstring.patch new file mode 100644 index 0000000000..cae987703f --- /dev/null +++ b/academic/treeviewx/cstring.patch @@ -0,0 +1,71 @@ +--- tv-0.5.1/ncl-2.0/src/charactersblock.cpp.orig 2017-08-13 08:38:11.451581249 +0700 ++++ tv-0.5.1/ncl-2.0/src/charactersblock.cpp 2017-08-13 08:38:25.267599533 +0700 +@@ -8,6 +8,7 @@ + #include "discretematrix.h" + #include "assumptionsblock.h" + #include "charactersblock.h" ++#include + + using namespace std; + +--- tv-0.5.1/ncl-2.0/src/nexus.cpp.orig 2017-08-13 08:40:07.443734383 +0700 ++++ tv-0.5.1/ncl-2.0/src/nexus.cpp 2017-08-13 08:40:17.625747774 +0700 +@@ -2,6 +2,7 @@ + #include "xnexus.h" + #include "nexustoken.h" + #include "nexus.h" ++#include + + #define NCL_NAME_AND_VERSION "NCL version 2.01" + #define NCL_COPYRIGHT "Copyright (c) 2000 by Paul O. Lewis" +--- tv-0.5.1/ncl-2.0/src/nexustoken.cpp.orig 2017-08-13 08:41:41.569857692 +0700 ++++ tv-0.5.1/ncl-2.0/src/nexustoken.cpp 2017-08-13 08:41:52.463871895 +0700 +@@ -1,6 +1,7 @@ + #include "nexusdefs.h" + #include "xnexus.h" + #include "nexustoken.h" ++#include + + using namespace std; + +--- tv-0.5.1/ncl-2.0/src/nxsstring.cpp.orig 2017-08-13 08:42:36.847929712 +0700 ++++ tv-0.5.1/ncl-2.0/src/nxsstring.cpp 2017-08-13 08:42:48.870945321 +0700 +@@ -20,6 +20,7 @@ + #include + #include + #include ++#include + #include "nxsstring.h" + + nxsstring& nxsstring::operator+=( const double d ) +--- tv-0.5.1/TreeLib/Parse.cpp.orig 2017-08-13 08:43:50.188024809 +0700 ++++ tv-0.5.1/TreeLib/Parse.cpp 2017-08-13 08:44:00.407038015 +0700 +@@ -23,6 +23,7 @@ + + #include + #include "Parse.h" ++#include + + // Return the next token in the string + tokentype Parser::NextToken () +--- tv-0.5.1/TreeLib/TreeLib.cpp.orig 2017-08-13 08:45:24.898146879 +0700 ++++ tv-0.5.1/TreeLib/TreeLib.cpp 2017-08-13 08:45:33.518157938 +0700 +@@ -23,6 +23,7 @@ + + #include "TreeLib.h" + #include "Parse.h" ++#include + + #include + +--- tv-0.5.1/TreeLib/treereader.cpp.orig 2017-08-13 08:47:09.041280171 +0700 ++++ tv-0.5.1/TreeLib/treereader.cpp 2017-08-13 08:51:04.192577614 +0700 +@@ -22,6 +22,8 @@ + // $Id: treereader.cpp,v 1.5 2003/09/10 12:58:16 rdmp1c Exp $ + + #include "treereader.h" ++#include ++#include + + #if __MWERKS__ + #include diff --git a/academic/treeviewx/doinst.sh b/academic/treeviewx/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/treeviewx/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/treeviewx/slack-desc b/academic/treeviewx/slack-desc new file mode 100644 index 0000000000..3d1a87af6b --- /dev/null +++ b/academic/treeviewx/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------------------------------------------------------| +treeviewx: treeviewx (Program to display phylogenetic trees) +treeviewx: +treeviewx: TreeView X provides a simple way to view the contents of a NEXUS, +treeviewx: PHYLIP, Hennig86, Clustal, or other format tree file. +treeviewx: +treeviewx: Home: http://code.google.com/p/treeviewx/ +treeviewx: +treeviewx: +treeviewx: +treeviewx: +treeviewx: diff --git a/academic/treeviewx/treeviewx.SlackBuild b/academic/treeviewx/treeviewx.SlackBuild new file mode 100644 index 0000000000..f229fe052f --- /dev/null +++ b/academic/treeviewx/treeviewx.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/sh + +# Slackware build script for treeviewx + +# Renamed to from "treeview" to "treeviewx" in 2018 to avoid confusion +# with Michael Eisen's TreeView for matrix-like display of expression data. + +# Copyright 2011-2018 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=treeviewx +SRCNAM=tv +VERSION=${VERSION:-0.5.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) export ARCH=i586 ;; + arm*) export ARCH=arm ;; + *) export ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION +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 {} \; + +# Disable SVG support. If you want it, you should build +# wxGTK or wxPython including svg from contrib/src/svg +# Then, of course comment the next line. +sed "s:USE_SVG=1:USE_SVG=0:" -i configure + +patch -p1 < $CWD/cstring.patch + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS -fpermissive" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --build=$ARCH-slackware-linux + +make +make install DESTDIR=$PKG + +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 + +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 +cp -a COPYING INSTALL $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References +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/treeviewx/treeviewx.desktop b/academic/treeviewx/treeviewx.desktop new file mode 100644 index 0000000000..ab8e3727c3 --- /dev/null +++ b/academic/treeviewx/treeviewx.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Categories=Education; +Exec=tv +Icon=treeviewx +Name=TreeView X +StartupNotify=false +Type=Application +GenericName= diff --git a/academic/treeviewx/treeviewx.info b/academic/treeviewx/treeviewx.info new file mode 100644 index 0000000000..09997ad2b9 --- /dev/null +++ b/academic/treeviewx/treeviewx.info @@ -0,0 +1,10 @@ +PRGNAM="treeviewx" +VERSION="0.5.1" +HOMEPAGE="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/" +DOWNLOAD="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz" +MD5SUM="07e1ed8873c5f19ded7294668233bae1" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="wxPython" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/treeviewx/treeviewx.png b/academic/treeviewx/treeviewx.png new file mode 100644 index 0000000000..fbdf9d2fcc Binary files /dev/null and b/academic/treeviewx/treeviewx.png differ -- cgit v1.2.3