[med-svn] r2634 - in trunk/packages/phylowin/trunk: . debian debian/patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Sun Nov 9 08:31:17 UTC 2008
Author: plessy
Date: 2008-11-09 08:31:16 +0000 (Sun, 09 Nov 2008)
New Revision: 2634
Added:
trunk/packages/phylowin/trunk/debian/
trunk/packages/phylowin/trunk/debian/README.Debian
trunk/packages/phylowin/trunk/debian/changelog
trunk/packages/phylowin/trunk/debian/compat
trunk/packages/phylowin/trunk/debian/control
trunk/packages/phylowin/trunk/debian/copyright
trunk/packages/phylowin/trunk/debian/docs
trunk/packages/phylowin/trunk/debian/examples
trunk/packages/phylowin/trunk/debian/menu
trunk/packages/phylowin/trunk/debian/patches/
trunk/packages/phylowin/trunk/debian/patches/10_split_CFLAGS_and_add_clean_in_Makefile.patch
trunk/packages/phylowin/trunk/debian/phylowin.desktop
trunk/packages/phylowin/trunk/debian/phylowin.doc-base
trunk/packages/phylowin/trunk/debian/phylowin.install
trunk/packages/phylowin/trunk/debian/reference
trunk/packages/phylowin/trunk/debian/rules
trunk/packages/phylowin/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications to trunk
Property changes on: trunk/packages/phylowin/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/phylowin/trunk/debian/README.Debian
===================================================================
--- trunk/packages/phylowin/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/phylowin/trunk/debian/README.Debian 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1,6 @@
+phylowin for Debian
+-------------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- Charles Plessy <plessy at debian.org> Sun, 09 Nov 2008 11:28:33 +0900
Added: trunk/packages/phylowin/trunk/debian/changelog
===================================================================
--- trunk/packages/phylowin/trunk/debian/changelog (rev 0)
+++ trunk/packages/phylowin/trunk/debian/changelog 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1,6 @@
+phylowin (20080307-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #395840)
+
+ -- Charles Plessy <plessy at debian.org> Sun, 09 Nov 2008 11:28:33 +0900
+
Added: trunk/packages/phylowin/trunk/debian/compat
===================================================================
--- trunk/packages/phylowin/trunk/debian/compat (rev 0)
+++ trunk/packages/phylowin/trunk/debian/compat 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1 @@
+7
Added: trunk/packages/phylowin/trunk/debian/control
===================================================================
--- trunk/packages/phylowin/trunk/debian/control (rev 0)
+++ trunk/packages/phylowin/trunk/debian/control 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1,32 @@
+Source: phylowin
+Section: non-free/science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy at debian.org>
+Build-Depends: cdbs, debhelper (>= 7), libvibrant6-dev, lesstif2-dev
+Standards-Version: 3.8.0
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/phylowin/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/phylowin/trunk/
+# Ask first
+#XS-Autobuild: yes
+Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html
+
+Package: phylowin
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: seaview
+Description: graphical interface for molecular phylogenetic inference
+ Phylo_win performs neighbor-joining, parsimony and maximum likelihood
+ methods and bootstrap with any of them. Many distances can be used including
+ Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy (1995), LogDet for
+ nucleotidic sequences, Poisson correction for protein sequences, Ka and Ks for
+ codon sequences. Species and sites to include in the analysis are selected by
+ mouse. Reconstructed trees can be drawn, edited, printed, stored and evaluated
+ according to numerous criteria.
+ .
+ If you use Phylo_win in a published work, please cite the following reference:
+ .
+ Galtier, N., Gouy, M. and Gautier, C. (1996) SeaView and Phylo_win, two
+ graphic tools for sequence alignment and molecular phylogeny. Comput. Applic.
+ Biosci., 12, 543-548.
Added: trunk/packages/phylowin/trunk/debian/copyright
===================================================================
--- trunk/packages/phylowin/trunk/debian/copyright (rev 0)
+++ trunk/packages/phylowin/trunk/debian/copyright 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1,34 @@
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=311
+Upstream-Name: Phylo_win
+Upstream-Maintainer: Nicolas GALTIER <galtier at biomserv.univ-lyon1.fr>
+Upstream-Source: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/phylo_win/phylowin.tar
+Disclaimer: This package is not part of the Debian operating system.
+ The phylo_win source and binary Debian packages are part of the "non-free" area
+ in our archive. The packages in this area are not part of the Debian system,
+ although they have been configured for use with Debian. We nevertheless
+ support the use of the phylo_win source and binary Debian pacakges and provide
+ infrastructure for non-free packages (such as our bug tracking system and
+ mailing lists).
+# Ask first
+#X-Non-Free-Autobuild: yes
+# The licence does not forbid Debian from using autobuilders to create binary
+# packages.
+X-Packaged-By: Charles Plessy <plessy at debian.org>
+X-Packaged-On: Sun, 09 Nov 2008 11:28:33 +0900
+
+Files: *
+Copyright:
+License:
+
+Files: dparspw.c pdist.c pparspw.c
+Copyright: © 1993 Joseph Felsenstein
+License: Phylip (non-DFSG compliant)
+ version 3.52c. (c) Copyright 1993 by Joseph Felsenstein.
+ Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe.
+ Permission is granted to copy and use this program provided no fee is
+ charged for it and provided that this copyright notice is not removed.
+
+Files: debian/*
+Copyright: © 2008 Charles Plessy <plessy at debian.org>
+License: PD
+ Please use these files as if they were in the public domain of your country.
Added: trunk/packages/phylowin/trunk/debian/docs
===================================================================
--- trunk/packages/phylowin/trunk/debian/docs (rev 0)
+++ trunk/packages/phylowin/trunk/debian/docs 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1 @@
+debian/reference
Added: trunk/packages/phylowin/trunk/debian/examples
===================================================================
--- trunk/packages/phylowin/trunk/debian/examples (rev 0)
+++ trunk/packages/phylowin/trunk/debian/examples 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1,2 @@
+DNA.mase
+protein.mase
Added: trunk/packages/phylowin/trunk/debian/menu
===================================================================
--- trunk/packages/phylowin/trunk/debian/menu (rev 0)
+++ trunk/packages/phylowin/trunk/debian/menu 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1,2 @@
+?package(phylowin):needs="X11|text|vc|wm" section="Applications/see-menu-manual"\
+ title="phylowin" command="/usr/bin/phylowin"
Added: trunk/packages/phylowin/trunk/debian/patches/10_split_CFLAGS_and_add_clean_in_Makefile.patch
===================================================================
--- trunk/packages/phylowin/trunk/debian/patches/10_split_CFLAGS_and_add_clean_in_Makefile.patch (rev 0)
+++ trunk/packages/phylowin/trunk/debian/patches/10_split_CFLAGS_and_add_clean_in_Makefile.patch 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1,31 @@
+Author: Charles Plessy
+Forwarded: Manolo Gouy
+Description: Splits CFLAGS (CDBS overrides them) and creates a cleaning target.
+Licence: as if public domain
+diff --git a/Makefile b/Makefile
+index 7cd7575..2d28a2c 100644
+--- a/Makefile
++++ b/Makefile
+@@ -20,15 +20,18 @@ lwlpw.o bionjpw.o nhmlpw.o simplex.o ajout_icone.o
+ SOURCES = phylo_win.c dparspw.c pparspw.c dmlpw.c pdist.c \
+ lwlpw.c bionjpw.c nhmlpw.c simplex.c ajout_icone.c
+
+-CFLAGS = -c -I$(VIBRANT)/include -I$(X11INCL) -DUNIX -DWIN_MOTIF $(OPT) $(DEBUG)
+-
++CFLAGS = -c $(OPT) $(DEBUG)
++CPPFLAGS = -DUNIX -DWIN_MOTIF
++INCLUDES = -I$(VIBRANT) -I$(X11INCL)
+
+ phylo_win : $(OBJECTS)
+ $(CC) -o $@ $(OBJECTS) \
+ -L$(VIBRANT)/lib -lvibrant -lncbi \
+ -L$(MOTIFLIB) -lXm -lMrm\
+ -L$(X11LIB) -lXt -lXmu -lXext -lX11 -lm $(DEBUG)
+-
++
++clean:
++ $(RM) *.o phylo_win
+
+ .c.o : $(SOURCES)
+- $(CC) $(CFLAGS) $?
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $?
Added: trunk/packages/phylowin/trunk/debian/phylowin.desktop
===================================================================
--- trunk/packages/phylowin/trunk/debian/phylowin.desktop (rev 0)
+++ trunk/packages/phylowin/trunk/debian/phylowin.desktop 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1,12 @@
+# This file was orignially written for Debian, and can be copied, used,
+# modified and redistributed under the same licence as Phylo_win itself.
+
+[Desktop Entry]
+Version=1.0
+Terminal=false
+Icon=phylo_win
+Exec=phylo_win %f
+Name=Phylo_win
+Type=Application
+Categories=Biology;Science;Education;
+MimeType=text/x-clustalw-alignment;
Added: trunk/packages/phylowin/trunk/debian/phylowin.doc-base
===================================================================
--- trunk/packages/phylowin/trunk/debian/phylowin.doc-base (rev 0)
+++ trunk/packages/phylowin/trunk/debian/phylowin.doc-base 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1,22 @@
+Document: phylowin
+Title: Debian phylowin Manual
+Author: <insert document author here>
+Abstract: This manual describes what phylowin is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/phylowin/phylowin.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/phylowin/phylowin.ps.gz
+
+Format: text
+Files: /usr/share/doc/phylowin/phylowin.text.gz
+
+Format: HTML
+Index: /usr/share/doc/phylowin/html/index.html
+Files: /usr/share/doc/phylowin/html/*.html
+
+
Added: trunk/packages/phylowin/trunk/debian/phylowin.install
===================================================================
--- trunk/packages/phylowin/trunk/debian/phylowin.install (rev 0)
+++ trunk/packages/phylowin/trunk/debian/phylowin.install 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1,2 @@
+phylo_win usr/bin
+debian/phylowin.desktop usr/share/applications
Added: trunk/packages/phylowin/trunk/debian/reference
===================================================================
--- trunk/packages/phylowin/trunk/debian/reference (rev 0)
+++ trunk/packages/phylowin/trunk/debian/reference 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1,12 @@
+ at article{N.Galtier12011996,
+author = {Galtier, N. and Gouy, M. and Gautier, C.},
+title = {{SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny}},
+journal = {Comput. Appl. Biosci.},
+volume = {12},
+number = {6},
+pages = {543-548},
+doi = {10.1093/bioinformatics/12.6.543},
+year = {1996},
+URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/12/6/543},
+eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/12/6/543.pdf}
+}
Added: trunk/packages/phylowin/trunk/debian/rules
===================================================================
--- trunk/packages/phylowin/trunk/debian/rules (rev 0)
+++ trunk/packages/phylowin/trunk/debian/rules 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+CFLAGS += -c
+CPPFLAGS += -DUNIX -DWIN_MOTIF
+DEB_MAKE_BUILD_TARGET = VIBRANT=/usr/include/ncbi
Property changes on: trunk/packages/phylowin/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/phylowin/trunk/debian/watch
===================================================================
--- trunk/packages/phylowin/trunk/debian/watch (rev 0)
+++ trunk/packages/phylowin/trunk/debian/watch 2008-11-09 08:31:16 UTC (rev 2634)
@@ -0,0 +1,23 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+# Uncomment to examine a Webpage
+# <Webpage URL> <string match>
+#http://www.example.com/downloads.php phylowin-(.*)\.tar\.gz
+
+# Uncomment to examine a Webserver directory
+#http://www.example.com/pub/phylowin-(.*)\.tar\.gz
+
+# Uncommment to examine a FTP server
+#ftp://ftp.example.com/pub/phylowin-(.*)\.tar\.gz debian uupdate
+
+# Uncomment to find new files on sourceforge, for devscripts >= 2.9
+# http://sf.net/phylowin/phylowin-(.*)\.tar\.gz
+
+# Uncomment to find new files on GooglePages
+# http://example.googlepages.com/foo.html phylowin-(.*)\.tar\.gz
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