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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> +DM-Upload-Allowed: yes +Uploaders: Charles Plessy <[EMAIL PROTECTED]> +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 <[EMAIL PROTECTED]> +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 <[EMAIL PROTECTED]> +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 <[EMAIL PROTECTED]> +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 @@ [EMAIL PROTECTED], +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
