diff options
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/treeviewx/README | 3 | ||||
| -rw-r--r-- | academic/treeviewx/cstring.patch | 71 | ||||
| -rw-r--r-- | academic/treeviewx/slack-desc | 2 | ||||
| -rw-r--r-- | academic/treeviewx/treeviewx.1 | 65 | ||||
| -rw-r--r-- | academic/treeviewx/treeviewx.SlackBuild | 25 | ||||
| -rw-r--r-- | academic/treeviewx/treeviewx.desktop | 2 | ||||
| -rw-r--r-- | academic/treeviewx/treeviewx.info | 8 |
7 files changed, 91 insertions, 85 deletions
diff --git a/academic/treeviewx/README b/academic/treeviewx/README index 9e1dcb3422..218f85f4cf 100644 --- a/academic/treeviewx/README +++ b/academic/treeviewx/README @@ -15,7 +15,8 @@ Some of its features include: Note! This program is different from Michael Eisen's TreeView for matrix- -like display of expression data. +like display of expression data. Also, we build the sources distributed +by Debian. For details and citation: Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic diff --git a/academic/treeviewx/cstring.patch b/academic/treeviewx/cstring.patch deleted file mode 100644 index cae987703f..0000000000 --- a/academic/treeviewx/cstring.patch +++ /dev/null @@ -1,71 +0,0 @@ ---- 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 <cstring> - - 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 <cstring> - - #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 <cstring> - - 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 <stdio.h> - #include <assert.h> - #include <math.h> -+#include <cstring> - #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 <ctype.h> - #include "Parse.h" -+#include <cstring> - - // 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 <cstdlib> - - #include <vector> - ---- 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 <cstring> -+#include <stdlib.h> - - #if __MWERKS__ - #include <string.h> diff --git a/academic/treeviewx/slack-desc b/academic/treeviewx/slack-desc index 3d1a87af6b..7130ac2dc0 100644 --- a/academic/treeviewx/slack-desc +++ b/academic/treeviewx/slack-desc @@ -11,7 +11,7 @@ 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: diff --git a/academic/treeviewx/treeviewx.1 b/academic/treeviewx/treeviewx.1 new file mode 100644 index 0000000000..e286165f47 --- /dev/null +++ b/academic/treeviewx/treeviewx.1 @@ -0,0 +1,65 @@ +'\" t +.\" Title: TREEVIEW X +.\" Author: [see the "AUTHOR" section] +.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/> +.\" Date: 06/23/2011 +.\" Manual: User Manuals +.\" Source: TreeView X 0.5 +.\" Language: English +.\" +.TH "TREEVIEW X" "1" "06/23/2011" "TreeView X 0.5" "User Manuals" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +TreeView_X \- displays and prints phylogenetic trees +.SH "SYNOPSIS" +.HP \w'\fBtv\fR\ 'u +\fBtv\fR [\fIfilename\fR] +.SH "DESCRIPTION" +.PP +\fBtv\fR +is the program that starts the TreeView X GUI\&. +.PP +TreeView X is an open source and multi\-platform program to display phylogenetic trees\&. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE\-PUZZLE, and other programs)\&. It allows one to order the branches of the trees, and to export the trees in SVG format\&. +.PP +If started from the command line with +filename +as an argument, TreeView X will open the tree stored in +filename\&. +.SH "SEE ALSO" +.PP +At present there is is no documentation for TreeView X\&. In the meantime please see the online documentation for TreeView (remember that TreeView X has only a subset of the features of TreeView)\&. http://taxonomy\&.zoology\&.gla\&.ac\&.uk/rod/treeview/treeview_manual\&.html +.SH "REFERENCE" +.PP +Page, R\&. D\&. M\&. 1996\&. TREEVIEW: An application to display phylogenetic trees on personal computers\&. Computer Applications in the Biosciences 12: 357\-358\&. +.SH "AUTHOR" +.PP +TreeView X +was written by Rod Page (r\&.page@bio\&.gla\&.ac\&.uk) URL: http://darwin\&.zoology\&.gla\&.ac\&.uk/~rpage/treeviewx\&. +.PP +This manual page was written by Charles Plessy (plessy@debian\&.org) for the +Debian(TM) +system (but may be used by others)\&. +.PP +Permission is granted to copy, distribute and/or modify TreeView\ \&X and this document under the terms of the +GNU +General Public License, Version 2 or any later version published by the Free Software Foundation\&. +.PP +On Debian systems, the complete text of the GNU General Public License version 2 can be found in /usr/share/common\-licenses/GPL\-2\&. diff --git a/academic/treeviewx/treeviewx.SlackBuild b/academic/treeviewx/treeviewx.SlackBuild index f229fe052f..5929e48f2d 100644 --- a/academic/treeviewx/treeviewx.SlackBuild +++ b/academic/treeviewx/treeviewx.SlackBuild @@ -5,7 +5,7 @@ # 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 +# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -27,7 +27,9 @@ PRGNAM=treeviewx SRCNAM=tv -VERSION=${VERSION:-0.5.1} +SRCVER=0.5 +VERSION=${VERSION:-0.5.1_20100723} +SRCDATE=20100823 BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -63,9 +65,9 @@ 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 +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/${PRGNAM}_${SRCVER}.1+${SRCDATE}.orig.tar.gz +cd $SRCNAM-$SRCVER chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -78,8 +80,6 @@ find -L . \ # 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="$SLKCFLAGS -fpermissive" \ ./configure \ @@ -93,9 +93,20 @@ CXXFLAGS="$SLKCFLAGS -fpermissive" \ make make install DESTDIR=$PKG +# Let's rename the executable +cd $PKG/usr/bin +mv $SRCNAM $PRGNAM +cd - + +# Thanks Debian for the man page +install -D -m644 $CWD/$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 + mkdir -p $PKG/usr/share/{applications,pixmaps} cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps diff --git a/academic/treeviewx/treeviewx.desktop b/academic/treeviewx/treeviewx.desktop index ab8e3727c3..2ef02ac0d0 100644 --- a/academic/treeviewx/treeviewx.desktop +++ b/academic/treeviewx/treeviewx.desktop @@ -1,6 +1,6 @@ [Desktop Entry] Categories=Education; -Exec=tv +Exec=treeviewx Icon=treeviewx Name=TreeView X StartupNotify=false diff --git a/academic/treeviewx/treeviewx.info b/academic/treeviewx/treeviewx.info index 09997ad2b9..8de22d44fb 100644 --- a/academic/treeviewx/treeviewx.info +++ b/academic/treeviewx/treeviewx.info @@ -1,8 +1,8 @@ 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" +VERSION="0.5.1_20100723" +HOMEPAGE="https://github.com/rdmpage" +DOWNLOAD="http://deb.debian.org/debian/pool/main/t/treeviewx/treeviewx_0.5.1+20100823.orig.tar.gz" +MD5SUM="8059a306b723e6fb4d3befcf302b2920" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="wxPython" |