debian/0000755000000000000000000000000012201001004007142 5ustar debian/README.Debian0000644000000000000000000000241711756700506011242 0ustar paml for Debian --------------- This packaging is still work in progress but should as the direct adaptation from the well respected and much used upstream source tree but sufficient for a redistribution in Debian. The preparation of man pages for the binaries and the doc-base description of the documentation has not yet been addressed. Help from the community would be much appreciated on those issues. Renamed executable: evolver --------------------------- A different package in Debian (namely evolver) ships a binary with the very same name and to avoid name space pollution the binary from the paml package needed to be renamed to /usr/bin/paml-evolver (if you disagree with this choice of name please help us to make Debian better and make a more appropriate suggestion.) If you are using this exectuable in scripts and you need to relay on the original name there is another option: Copy the directory /usr/share/doc/paml/profile.d to /etc/profile.d and by doing so enable setting the PATH variable to prefer the PATH /usr/lib/debian-med/bin over /usr/bin. There the original name is conserved. Please note that this might hide the binary contained in the evolver package from all users of your computer. -- Andreas Tille Tue, 15 May 2012 11:10:59 +0200 debian/profile.d/0000755000000000000000000000000011754423565011064 5ustar debian/profile.d/paml0000644000000000000000000000022311754423565011735 0ustar # set PATH to enable finding paml executables with original name # install this file to /etc/profile.d export PATH="/usr/lib/debian-med/bin:$PATH" debian/paml.links0000644000000000000000000000047111754416615011175 0ustar usr/lib/debian-med/bin/baseml usr/bin/baseml usr/lib/debian-med/bin/basemlg usr/bin/basemlg usr/lib/debian-med/bin/chi2 usr/bin/chi2 usr/lib/debian-med/bin/codeml usr/bin/codeml usr/lib/debian-med/bin/evolver usr/bin/paml-evolver usr/lib/debian-med/bin/pamp usr/bin/pamp usr/lib/debian-med/bin/yn00 usr/bin/yn00 debian/source/0000755000000000000000000000000011641335477010501 5ustar debian/source/format0000644000000000000000000000001411441637541011702 0ustar 3.0 (quilt) debian/paml.docs0000644000000000000000000000005411756700033010772 0ustar GeneticCode.txt README.txt debian/profile.d debian/README.source0000644000000000000000000000065612201000410011330 0ustar paml for Debian --------------- The source code ships with PDFs that have their sources not shipped with the sources code. Given that the package is non-free anyway, those have been left in. The Windows binaries have been removed from the source tree by using debian/rules get-orig-source and the enhanced uscan (see comment in debian/rules) Some source files are dos-formatted. While annoying, this has not been changed. debian/copyright0000644000000000000000000000134212200776551011126 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://abacus.gene.ucl.ac.uk/software/paml.html Files-Excluded: bin/*.exe Technical/Simulation/*.exe Technical/Simulation/Codon/*.exe Files: * Copyright: © 1992-2013 Ziheng Yang License: PAML-From-the-home-page-2010-09-08 PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. Comment: The author and copyright holder has agreed to the redistribution of PAML by Debian. Files: debian/* Copyright: © 2010 Pjotr Prins License: GPL-3 see "/usr/share/common-licenses/GPL-3". debian/upstream0000644000000000000000000000056011754655310010761 0ustar Reference: Author: Ziheng Yang Title: "PAML 4: phylogenetic analysis by maximum likelihood" Journal: Molecular Biology and Evolution Year: 2007 Volume: 24 Number: 8 Pages: 1586-91 DOI: 10.1093/molbev/msm088 PMID: 17483113 URL: http://mbe.oxfordjournals.org/content/24/8/1586 eprint: http://mbe.oxfordjournals.org/content/24/8/1586.full.pdf+html debian/rules0000755000000000000000000000123212200776662010254 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 override_dh_installexamples: dh_installexamples for d in `find debian -name examples -a -type d`; do \ find $$d \! -type d | xargs -r chmod -x ; \ done %: dh $@ override_dh_builddeb: dh_builddeb -- -Z xz # Remark: The following uscan command requires devscripts > 2.12.4 which is not # yet released at the time of this package release. The code can be obtained # via # git clone git://tille@git.debian.org/git/users/tille/devscripts.git # and then use scripts/uscan.pl get-orig-source: uscan --verbose --force-download --repack-compression xz debian/patches/0000755000000000000000000000000012200775657010630 5ustar debian/patches/hardening.patch0000644000000000000000000000366012200775657013615 0ustar Description: Enable propagation of hardening flags Author: Andreas Tille Date: Tue, 15 May 2012 11:10:59 +0200 --- a/src/Makefile +++ b/src/Makefile @@ -1,7 +1,7 @@ PRGS = baseml codeml basemlg mcmctree pamp evolver yn00 chi2 CC = cc # cc, gcc, cl -CFLAGS = -O4 -funroll-loops -fomit-frame-pointer -finline-functions +CFLAGS += -O4 -funroll-loops -fomit-frame-pointer -finline-functions #MAC OSX G5: #CFLAGS = -mcpu=G5 -O4 -funroll-loops -fomit-frame-pointer -finline-functions @@ -20,21 +20,21 @@ LIBS = -lm # -lM all : $(PRGS) baseml : baseml.c tools.c treesub.c treespace.c paml.h - $(CC) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS) + $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ baseml.c tools.c $(LIBS) basemlg : basemlg.c tools.c treesub.c treespace.c paml.h - $(CC) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS) + $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ basemlg.c tools.c $(LIBS) codeml : codeml.c tools.c treesub.c treespace.c paml.h - $(CC) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS) + $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ codeml.c tools.c $(LIBS) evolver : evolver.c tools.c treesub.c treespace.c paml.h - $(CC) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS) + $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ evolver.c tools.c $(LIBS) pamp : pamp.c tools.c treesub.c treespace.c paml.h - $(CC) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS) + $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ pamp.c tools.c $(LIBS) mcmctree : mcmctree.c tools.c treesub.c treespace.c paml.h - $(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS) + $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ mcmctree.c tools.c $(LIBS) yn00: yn00.c tools.c paml.h - $(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS) + $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ yn00.c tools.c $(LIBS) chi2 : chi2.c - $(CC) $(CFLAGS) -o $@ chi2.c $(LIBS) + $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ chi2.c $(LIBS) PREFIX=/usr DESTDIR=/ debian/patches/series0000644000000000000000000000003711756701561012043 0ustar makefile.patch hardening.patch debian/patches/makefile.patch0000644000000000000000000000140112200775653013416 0ustar Description: Simplify building by creating main Makefile and install target for src/Makefile Author: Pjotr Prins Date: Tue, 07 Sep 2010 21:09:02 +0200 --- /dev/null +++ b/Makefile @@ -0,0 +1,9 @@ + +all install build: + echo "Executing make $@ in src directory, instead." + make -C src $@ + +clean: + echo "Cleaning binaries" + rm -f $(find src -name "*.c" | sed -e 's/.c$//') + --- a/src/Makefile +++ b/src/Makefile @@ -35,3 +35,11 @@ yn00: yn00.c tools.c paml.h $(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS) chi2 : chi2.c $(CC) $(CFLAGS) -o $@ chi2.c $(LIBS) + +PREFIX=/usr +DESTDIR=/ + +install: + if [ ! -d "$(DESTDIR)/$(PREFIX)/bin" ]; then mkdir -p "$(DESTDIR)/$(PREFIX)/bin"; fi + cp $(PRGS) $(DESTDIR)/$(PREFIX)/bin/ + debian/watch0000644000000000000000000000016711754417516010236 0ustar version=3 http://abacus.gene.ucl.ac.uk/software/paml.html paml([0-9a-z.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))|zip) debian/changelog0000644000000000000000000000466512201001004011027 0ustar paml (4.7-1) unstable; urgency=low * New upstream version * debian/control: - cme fix dpkg-control - use anonscm in Vcs fields * debian/rules: provide get-orig-source target to make use of new uscan to remove windows binaries -- Andreas Tille Thu, 08 Aug 2013 22:07:27 +0200 paml (4.5-1) unstable; urgency=low [ Pjotr Prins ] * Improved long description. [ Andreas Tille ] * New upstream version * Fixed watch file * debian/control: Standards-Version: 3.9.3 (no changes needed) * debian/rules: remove useless dh-make template * debian/paml.dirs: removed because unneeded * debian/{install,links}: install all binaries to /usr/lib/debian-med/bin and symlink to /usr/bin with the exception of evolver which has a name space conflict. This is renamed to /usr/bin/paml-evolver Closes: #661519 * debian/{paml.docs,paml-doc.docs}: - Adapted to new names - do not duplicate the same files into both packages (paml and paml-doc) * debian/profile.d/paml: Set PATH to find paml executables under their expected names * debian/README.Debian: Document the name space conflict solution * debian/upstream: Citation information * debhelper 9 (control+compat) * debian/patches/hardening.patch: Enable propagation of hardening flags -- Andreas Tille Tue, 15 May 2012 11:10:59 +0200 paml (4.4e-1) unstable; urgency=low * Team upload. * New upstream release. * Upload to unstable (Closes: #643843). * Corrected debian/watch for downloading sources with uscan. * Removed links to inexsistant Git repositories in debian/README.source. * Corrected VCS URLs (debian/control). * Conforms to Policy 3.9.2 (debian/control, no other changes needed). * Use Debhelper 8 (debian/control, debian/compat). * Converted debian/copyright to machine readable format version 1.0. * Compress binary packages with xz. -- Charles Plessy Fri, 30 Sep 2011 21:48:20 +0900 paml (4.4c-3) experimental; urgency=low * doc -> non-free/doc (Closes: #608530). -- Steffen Moeller Sat, 01 Jan 2011 13:56:50 +0100 paml (4.4c-2) experimental; urgency=low * Adjusting for non-free section. -- Pjotr Prins Sat, 11 Sep 2010 23:01:37 +0200 paml (4.4c-1) experimental; urgency=low * Initial release (Closes: #595958). -- Pjotr Prins Tue, 07 Sep 2010 21:09:02 +0200 debian/paml-doc.docs0000644000000000000000000000000611754422324011534 0ustar doc/* debian/compat0000644000000000000000000000000211756700600010366 0ustar 9 debian/paml.install0000644000000000000000000000040711754416400011512 0ustar usr/bin/baseml usr/lib/debian-med/bin usr/bin/basemlg usr/lib/debian-med/bin usr/bin/chi2 usr/lib/debian-med/bin usr/bin/codeml usr/lib/debian-med/bin usr/bin/evolver usr/lib/debian-med/bin usr/bin/pamp usr/lib/debian-med/bin usr/bin/yn00 usr/lib/debian-med/bin debian/control0000644000000000000000000000203612201000726010560 0ustar Source: paml Maintainer: Debian Med Packaging Team Uploaders: Pjotr Prins , Steffen Moeller , Andreas Tille Section: non-free/science Priority: extra Build-Depends: debhelper (>= 9) Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/paml/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/paml/trunk/ Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html Package: paml Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: Phylogenetic Analysis by Maximum Likelihood (PAML) PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Package: paml-doc Architecture: all Section: non-free/doc Depends: ${misc:Depends} Description: Documentation for PAML The source code comes with a series of PDF files to help with further insights for the working of, and with, PAML. debian/paml-doc.examples0000644000000000000000000000001311443341140012407 0ustar examples/*