--- exonerate-1.4.0.orig/debian/control +++ exonerate-1.4.0/debian/control @@ -0,0 +1,22 @@ +Source: exonerate +Section: science +Priority: optional +Maintainer: Debian-Med Packaging Team +Uploaders: Steffen Moeller , Charles Plessy +Build-Depends: debhelper (>= 5), autotools-dev, libglib1.2-dev +Standards-Version: 3.7.2 +XS-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/exonerate/trunk/ +XS-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/exonerate +Homepage: http://www.ebi.ac.uk/~guy/exonerate/ + +Package: exonerate +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: wise +Description: tool for comparison of long biological sequences + Much of the functionality of the Wise dynamic programming + suite was reimplemented in C for better efficiency. + Exonerate is an intrinsic component of the building of + the Ensembl genome databases, providing similarity + scores between RNA and DNA sequences and thus determining + splice variants and coding sequences in general. --- exonerate-1.4.0.orig/debian/links +++ exonerate-1.4.0/debian/links @@ -0,0 +1,25 @@ +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/exonerate-client.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/exonerate-server.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fasta2esd.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastaannotatecdna.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastachecksum.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastaclean.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastaclip.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastacomposition.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastadiff.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastaexplode.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastafetch.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastahardmask.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastaindex.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastalength.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastanrdb.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastareformat.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastaremove.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastarevcomp.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastasoftmask.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastasort.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastasplit.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastasubseq.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastatranslate.1.gz +usr/share/man/man1/fastaoverlap.1.gz usr/share/man/man1/fastavalidcds.1.gz + --- exonerate-1.4.0.orig/debian/dirs +++ exonerate-1.4.0/debian/dirs @@ -0,0 +1 @@ +usr/bin --- exonerate-1.4.0.orig/debian/compat +++ exonerate-1.4.0/debian/compat @@ -0,0 +1 @@ +5 --- exonerate-1.4.0.orig/debian/exonerate.manpages +++ exonerate-1.4.0/debian/exonerate.manpages @@ -0,0 +1,3 @@ +doc/man/man1/exonerate.1 +doc/man/man1/ipcress.1 +debian/manpages/fastaoverlap.1 --- exonerate-1.4.0.orig/debian/watch +++ exonerate-1.4.0/debian/watch @@ -0,0 +1,3 @@ +version=3 +http://www.ebi.ac.uk/~guy/exonerate/exonerate-([0-9.]*)\.tar\.gz + --- exonerate-1.4.0.orig/debian/changelog +++ exonerate-1.4.0/debian/changelog @@ -0,0 +1,6 @@ +exonerate (1.4.0-1) unstable; urgency=low + + * Initial release (Closes: #431404). + + -- Steffen Moeller Mon, 02 Jul 2007 11:42:38 +0200 + --- exonerate-1.4.0.orig/debian/copyright +++ exonerate-1.4.0/debian/copyright @@ -0,0 +1,38 @@ +This package was debianized by Steffen Moeller on +Mon, 02 Jul 2007 11:42:38 +0200. + +It was downloaded from http://www.ebi.ac.uk/~guy/exonerate/ + +Upstream Author: + + Guy St. C. Slater + +Copyright: + + Copyright (C) 2000-2006 Guy St. C. Slater + +License: + + This package is free software; you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public + License as published by the Free Software Foundation; either + version 2 of the License, or (at your option) any later version. + + This package is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with this package; if not, write to the Free Software + Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + +On Debian systems, the complete text of the GNU Lesser General +Public License can be found in `/usr/share/common-licenses/LGPL'. +The source code of this package links to the web URL indicating +to version 3 of the license. The author is likely not to have been +aware of the new version at the time the source code was released. +The version distributed with the source is an earlier version. + +The Debian packaging is (C) 2007, Steffen Moeller and +is licensed under the LGPL, see `/usr/share/common-licenses/LGPL'. --- exonerate-1.4.0.orig/debian/docs +++ exonerate-1.4.0/debian/docs @@ -0,0 +1,4 @@ +NEWS +README +TODO +AUTHORS --- exonerate-1.4.0.orig/debian/rules +++ exonerate-1.4.0/debian/rules @@ -0,0 +1,116 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# Sample debian/rules that uses debhelper. +# This file was originally written by Joey Hess and Craig Small. +# As a special exception, when this file is copied by dh-make into a +# dh-make output file, you may use that output file without restriction. +# This special exception was added by Craig Small in version 0.37 of dh-make. + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + + +# These are used for cross-compiling and for saving the configure script +# from having to guess our platform (since we know it already) +#DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE) +#DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE) + + +CFLAGS = -Wall -g + +ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) + CFLAGS += -O0 +else + CFLAGS += -O2 +endif + +config.status: configure + dh_testdir + # Add here commands to configure the package. +ifneq "$(wildcard /usr/share/misc/config.sub)" "" + cp -f /usr/share/misc/config.sub config.sub +endif +ifneq "$(wildcard /usr/share/misc/config.guess)" "" + cp -f /usr/share/misc/config.guess config.guess +endif + ./configure --host="$(DEB_HOST_GNU_TYPE)" \ + --build="$(DEB_BUILD_GNU_TYPE)" \ + --prefix=/usr \ + --mandir=\$${prefix}/share/man \ + --infodir=\$${prefix}/share/info \ + CFLAGS="$(CFLAGS)" + #--disable-glib2 + + #./configure --host="$(DEB_HOST_GNU_TYPE)" --build="$(DEB_BUILD_GNU_TYPE)" --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info CFLAGS="$(CFLAGS)" LDFLAGS="-Wl,-z,defs" + + +build: build-stamp + +build-stamp: config.status + dh_testdir + + # Add here commands to compile the package. + $(MAKE) + #docbook-to-man debian/exonerate.sgml > exonerate.1 + + touch $@ + +clean: + dh_testdir + dh_testroot + rm -f build-stamp + + # Add here commands to clean up after the build process. + [ ! -f Makefile ] || $(MAKE) distclean + rm -f config.sub config.guess + rm -rf codegen + + dh_clean + +install: build + dh_testdir + dh_testroot + dh_clean -k + dh_installdirs + + # Add here commands to install the package into debian/exonerate. + $(MAKE) DESTDIR=$(CURDIR)/debian/exonerate install + + +# Build architecture-independent files here. +binary-indep: build install +# We have nothing to do by default. + +# Build architecture-dependent files here. +binary-arch: build install + dh_testdir + dh_testroot + dh_installchangelogs ChangeLog + dh_installdocs + dh_installexamples +# dh_install +# dh_installmenu +# dh_installdebconf +# dh_installlogrotate +# dh_installemacsen +# dh_installpam +# dh_installmime +# dh_python +# dh_installinit +# dh_installcron +# dh_installinfo + dh_installman # Installs three manpages + dh_link # Makes symlinks to a common manpage + dh_strip + dh_compress + dh_fixperms +# dh_perl +# dh_makeshlibs + dh_installdeb + dh_shlibdeps + dh_gencontrol + dh_md5sums + dh_builddeb + +binary: binary-indep binary-arch +.PHONY: build clean binary-indep binary-arch binary install --- exonerate-1.4.0.orig/debian/manpages/fastaoverlap.1 +++ exonerate-1.4.0/debian/manpages/fastaoverlap.1 @@ -0,0 +1,122 @@ +.\" Hey, EMACS: -*- nroff -*- +.\" First parameter, NAME, should be all caps +.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection +.\" other parameters are allowed: see man(7), man(1) +.TH EXONERATE 1 "30 Jun 2007" +.\" Please adjust this date whenever revising the manpage. +.\" +.\" Some roff macros, for reference: +.\" .nh disable hyphenation +.\" .hy enable hyphenation +.\" .ad l left justify +.\" .ad b justify to both left and right margins +.\" .nf disable filling +.\" .fi enable filling +.\" .br insert line break +.\" .sp insert n+1 empty lines +.\" for manpage-specific macros, see man(7) +.SH NAME +exonerate \- suite for investigating DNA and RNA sequence similarities +.SH SYNOPSIS +.B exonerate-client +.RI [ --help ] +.br +.B exonerate-server +.RI [ --help ] +.br +.B fasta2esd +.RI [ --help ] +.br +.B fastaannotatecdna +.RI [ --help ] +.br +.B fastachecksum +.RI [ --help ] +.br +.B fastaclean +.RI [ --help ] +.br +.B fastaclip +.RI [ --help ] +.br +.B fastacomposition +.RI [ --help ] +.br +.B fastadiff +.RI [ --help ] +.br +.B fastaexplode +.RI [ --help ] +.br +.B fastafetch +.RI [ --help ] +.br +.B fastahardmask +.RI [ --help ] +.br +.B fastaindex +.RI [ --help ] +.br +.B fastalength +.RI [ --help ] +.br +.B fastanrdb +.RI [ --help ] +.br +.B fastaoverlap +.RI [ --help ] +.br +.B fastareformat +.RI [ --help ] +.br +.B fastaremove +.RI [ --help ] +.br +.B fastarevcomp +.RI [ --help ] +.br +.B fastasoftmask +.RI [ --help ] +.br +.B fastasort +.RI [ --help ] +.br +.B fastasplit +.RI [ --help ] +.br +.B fastasubseq +.RI [ --help ] +.br +.B fastatranslate +.RI [ --help ] +.br +.B fastavalidcds +.RI [ --help ] +.br +.SH DESCRIPTION +These programs are not described by the upstream author, however, some information +is available via the --help and -h arguments for all these programs. Whoever is using +any of these programs in routine, is requested to provide a seed of a respective man page +to the upstream author. +.PP +.SH OPTIONS +.TP +.B \-h, +.B \-\-help +Show summary of options. +.TP +.B \-v, \-\-version +Show version of program. +.SH SEE ALSO +.BR http://www.ebi.ac.uk/~guy/exonerate/ +.br +The author of this package provides a beginner ( +.IR http://www.ebi.ac.uk/~guy/exonerate/beginner.html +) and and avanced +.RI http://www.ebi.ac.uk/~guy/exonerate/advanced.html +) tutorial on his web pages. +.SH AUTHOR +exonerate was written by Guy Slater . +.PP +This manual page was written by Steffen Moeller +for the Debian project (but may be used by others). --- exonerate-1.4.0.orig/debian/README.Debian +++ exonerate-1.4.0/debian/README.Debian @@ -0,0 +1,16 @@ +exonerate for Debian +-------------------- + +Charles has fixed the man pages for this package - many thanks to him. + +The upstream author, Guy Slater, is very supportive of Debian. He even +gave brief instructions on how to build a package in his README. +This is much appreciated. + +Guy was contacted asking for a clarification of the version of the +GPL he refers to and to avoid the web link in the C sources to a (now) +later version than he distributes with the source. + +Steffen + + -- Steffen Moeller Mon, 02 Jul 2007 11:42:38 +0200