Commit 08d71f98 authored by Thomas Schiex's avatar Thomas Schiex
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Merge branch 'cvsmodule-Debianization'

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=======================
Debianization of eugene
=======================
Content of the directory
------------------------
Binary and source files of the debian package inra-eugene:
inra-eugene_3.2-1.diff.gz
inra-eugene_3.2-1.dsc
inra-eugene_3.2-1_i386.build
inra-eugene_3.2-1_i386.changes
inra-eugene_3.2-1_i386.deb
inra-eugene_3.2.orig.tar.gz
Memory of the original debian directory:
debian
How to build the package inra-eugene
------------------------------------
1. Copy a eugene-<no>.tar.gz distribution of eugene and extract it
2. Move eugene-<no> in inra-eugene-<no> directory
(be sure to have the last Makefile.am and .in that
does not provide execute permision when no necessary,
this avoid a lintian warning)
4. Go in the inra-eugene-<no> directory and execute:
dh_make --copyright artistic -e cros@ossau.toulouse.inra.fr -s
5. Update the inra-eugene-<no>/debian directory
If minor modifications were done, remove the created debian directory
and copy Debianization/debian directory at the same place.
Note that updating the files changelog and copyrigth (if <no> has changed)
may be sufficient.
6. Empty environnement variables: CFLAGS, CXXFLAGS, CPPFLAGS
7. debuild -rfakeroot --preserve-env
Note that the following packages need to be installed:
* dh-make (for dh_make)
* devscript (for debuild)
* lintian
* fakeroot
* gnupg (generation of a key with gpg --gen-key)
It is possible to test the installation with:
dpkg -i inra-eugene_<no>-1_i386.deb
eugene doc/Sequences/SYNO_ARATH.fasta
dpkg -r inra-eugene
What remains
------------
1. Check of the Build-Depends defined in the debian/control file
2. Improve of the man documentation
3. Remove of the warning "Compatibility levels before 3 are deprecated."
appeared with the 3.3 packaging.
inra-eugene (3.3-1) unstable; urgency=low
* Initial release.
-- Marie-Josee Cros <cros@ossau.toulouse.inra.fr> Fri, 2 Sep 2005 11:45:49 +0200
Source: inra-eugene
Section: science
Priority: optional
Maintainer: Marie-Josee Cros <cros@ossau.toulouse.inra.fr>
Build-Depends: debhelper (>= 4.0.0), libstdc++5 (>= 1 ), libc6 (>= 2.3.2.ds1-20 ), libgd2 (>= 2.0.33-1.1 )
Standards-Version: 3.6.1
Package: inra-eugene
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: [Biology] A gene finder for Eukaryotics
eugene is an open gene finder for eukaryotic organisms.
Compared to most existing gene finders, it is characterized by
its ability to simply integrate arbitrary sources of information
in its prediction process.
.
Contact: eugene@ossau.toulouse.inra.fr
This package was debianized by Marie-Josee Cros <cros@ossau.toulouse.inra.fr> on
Fri, 2 Sep 2005 11:45:49 +0200.
It was downloaded from this web page http://mulcyber.toulouse.inra.fr/project/showfiles.php?group_id=10
Copyright:
Upstream Authors: EuGene Team (see the web site for the description)
License:
This program is free software; you can redistribute it and/or modify it
under the terms of the "Artistic License" which comes with Debian.
THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
On Debian systems, the complete text of the Artistic License
can be found in `/usr/share/common-licenses/Artistic'.
<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
<!-- Process this file with docbook-to-man to generate an nroff manual
page: `docbook-to-man manpage.sgml > manpage.1'. You may view
the manual page with: `docbook-to-man manpage.sgml | nroff -man |
less'. A typical entry in a Makefile or Makefile.am is:
manpage.1: manpage.sgml
docbook-to-man $< > $@
The docbook-to-man binary is found in the docbook-to-man package.
Please remember that if you create the nroff version in one of the
debian/rules file targets (such as build), you will need to include
docbook-to-man in your Build-Depends control field.
-->
<!-- Fill in your name for FIRSTNAME and SURNAME. -->
<!ENTITY dhfirstname "<firstname>EuGene</firstname>">
<!ENTITY dhsurname "<surname>Team</surname>">
<!-- Please adjust the date whenever revising the manpage. -->
<!ENTITY dhdate "<date>April 1, 2005</date>">
<!-- SECTION should be 1-8, maybe w/ subsection other parameters are
allowed: see man(7), man(1). -->
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>eugene@ossau.toulouse.inra.fr</email>">
<!ENTITY dhusername "Marie-Josee Cros">
<!ENTITY dhucpackage "<refentrytitle>INRA-EUGENE</refentrytitle>">
<!ENTITY dhpackage "inra-eugene">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
]>
<refentry>
<refentryinfo>
<address>
&dhemail;
</address>
<author>
&dhfirstname;
&dhsurname;
</author>
<copyright>
<year>2003</year>
<holder>&dhusername;</holder>
</copyright>
&dhdate;
</refentryinfo>
<refmeta>
&dhucpackage;
&dhsection;
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose> Estimation of parameters (inspired of Glimmer (Salzberg))</refpurpose>
</refnamediv>
<refsect1>
<title>DESCRIPTION</title>
<para>This manual page was written for the &debian; distribution
because the original program does not have a manual page.</para>
<para><command>&dhpackage;</command> This program is related to the eugene software.</para>
</refsect1>
<refsect1>
<title>SEE ALSO</title>
<para>eugene (1).</para>
</refsect1>
<refsect1>
<title>AUTHOR</title>
<para>This manual page was written by &dhusername; &dhemail; for
the &debian; system (but may be used by others). Permission is
granted to copy, distribute and/or modify this document under
the terms of the &gnu; General Public License, Version 2 any
later version published by the Free Software Foundation.
</para>
<para>
On Debian systems, the complete text of the GNU General Public
License can be found in /usr/share/common-licenses/GPL.
</para>
</refsect1>
</refentry>
<!-- Keep this comment at the end of the file
Local variables:
mode: sgml
sgml-omittag:t
sgml-shorttag:t
sgml-minimize-attributes:nil
sgml-always-quote-attributes:t
sgml-indent-step:2
sgml-indent-data:t
sgml-parent-document:nil
sgml-default-dtd-file:nil
sgml-exposed-tags:nil
sgml-local-catalogs:nil
sgml-local-ecat-files:nil
End:
-->
<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
<!-- Process this file with docbook-to-man to generate an nroff manual
page: `docbook-to-man manpage.sgml > manpage.1'. You may view
the manual page with: `docbook-to-man manpage.sgml | nroff -man |
less'. A typical entry in a Makefile or Makefile.am is:
manpage.1: manpage.sgml
docbook-to-man $< > $@
The docbook-to-man binary is found in the docbook-to-man package.
Please remember that if you create the nroff version in one of the
debian/rules file targets (such as build), you will need to include
docbook-to-man in your Build-Depends control field.
-->
<!-- Fill in your name for FIRSTNAME and SURNAME. -->
<!ENTITY dhfirstname "<firstname>EuGene</firstname>">
<!ENTITY dhsurname "<surname>Team</surname>">
<!-- Please adjust the date whenever revising the manpage. -->
<!ENTITY dhdate "<date>April 1, 2005</date>">
<!-- SECTION should be 1-8, maybe w/ subsection other parameters are
allowed: see man(7), man(1). -->
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>eugene@ossau.toulouse.inra.fr</email>">
<!ENTITY dhusername "Marie-Josee Cros">
<!ENTITY dhucpackage "<refentrytitle>INRA-EUGENE</refentrytitle>">
<!ENTITY dhpackage "inra-eugene">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
]>
<refentry>
<refentryinfo>
<address>
&dhemail;
</address>
<author>
&dhfirstname;
&dhsurname;
</author>
<copyright>
<year>2003</year>
<holder>&dhusername;</holder>
</copyright>
&dhdate;
</refentryinfo>
<refmeta>
&dhucpackage;
&dhsection;
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose> This program build a Weight Array Model (WAM) for a WAM eugene sensor.</refpurpose>
</refnamediv>
<refsect1>
<title>DESCRIPTION</title>
<para>This manual page was written for the &debian; distribution
because the original program does not have a manual page.</para>
<para><command>&dhpackage;</command> This program is related to the eugene software.</para>
</refsect1>
<refsect1>
<title>SEE ALSO</title>
<para>eugene (1).</para>
</refsect1>
<refsect1>
<title>AUTHOR</title>
<para>This manual page was written by &dhusername; &dhemail; for
the &debian; system (but may be used by others). Permission is
granted to copy, distribute and/or modify this document under
the terms of the &gnu; General Public License, Version 2 any
later version published by the Free Software Foundation.
</para>
<para>
On Debian systems, the complete text of the GNU General Public
License can be found in /usr/share/common-licenses/GPL.
</para>
</refsect1>
</refentry>
<!-- Keep this comment at the end of the file
Local variables:
mode: sgml
sgml-omittag:t
sgml-shorttag:t
sgml-minimize-attributes:nil
sgml-always-quote-attributes:t
sgml-indent-step:2
sgml-indent-data:t
sgml-parent-document:nil
sgml-default-dtd-file:nil
sgml-exposed-tags:nil
sgml-local-catalogs:nil
sgml-local-ecat-files:nil
End:
-->
<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
<!-- Process this file with docbook-to-man to generate an nroff manual
page: `docbook-to-man manpage.sgml > manpage.1'. You may view
the manual page with: `docbook-to-man manpage.sgml | nroff -man |
less'. A typical entry in a Makefile or Makefile.am is:
manpage.1: manpage.sgml
docbook-to-man $< > $@
The docbook-to-man binary is found in the docbook-to-man package.
Please remember that if you create the nroff version in one of the
debian/rules file targets (such as build), you will need to include
docbook-to-man in your Build-Depends control field.
-->
<!-- Fill in your name for FIRSTNAME and SURNAME. -->
<!ENTITY dhfirstname "<firstname>EuGene</firstname>">
<!ENTITY dhsurname "<surname>Team</surname>">
<!-- Please adjust the date whenever revising the manpage. -->
<!ENTITY dhdate "<date>April 1, 2005</date>">
<!-- SECTION should be 1-8, maybe w/ subsection other parameters are
allowed: see man(7), man(1). -->
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>eugene@ossau.toulouse.inra.fr</email>">
<!ENTITY dhusername "Marie-Josee Cros">
<!ENTITY dhucpackage "<refentrytitle>INRA-EUGENE</refentrytitle>">
<!ENTITY dhpackage "inra-eugene">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
]>
<refentry>
<refentryinfo>
<address>
&dhemail;
</address>
<author>
&dhfirstname;
&dhsurname;
</author>
<copyright>
<year>2003</year>
<holder>&dhusername;</holder>
</copyright>
&dhdate;
</refentryinfo>
<refmeta>
&dhucpackage;
&dhsection;
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose> This program can build a proteic markov model file for eugene
// from a proteic data base file in multifasta format (typicaly SwissProt).</refpurpose>
</refnamediv>
<refsect1>
<title>DESCRIPTION</title>
<para>This manual page was written for the &debian; distribution
because the original program does not have a manual page.</para>
<para><command>&dhpackage;</command> This program is related to the eugene software.</para>
</refsect1>
<refsect1>
<title>SEE ALSO</title>
<para>eugene (1).</para>
</refsect1>
<refsect1>
<title>AUTHOR</title>
<para>This manual page was written by &dhusername; &dhemail; for
the &debian; system (but may be used by others). Permission is
granted to copy, distribute and/or modify this document under
the terms of the &gnu; General Public License, Version 2 any
later version published by the Free Software Foundation.
</para>
<para>
On Debian systems, the complete text of the GNU General Public
License can be found in /usr/share/common-licenses/GPL.
</para>
</refsect1>
</refentry>
<!-- Keep this comment at the end of the file
Local variables:
mode: sgml
sgml-omittag:t
sgml-shorttag:t
sgml-minimize-attributes:nil
sgml-always-quote-attributes:t
sgml-indent-step:2
sgml-indent-data:t
sgml-parent-document:nil
sgml-default-dtd-file:nil
sgml-exposed-tags:nil
sgml-local-catalogs:nil
sgml-local-ecat-files:nil
End:
-->
<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
<!-- Process this file with docbook-to-man to generate an nroff manual
page: `docbook-to-man manpage.sgml > manpage.1'. You may view
the manual page with: `docbook-to-man manpage.sgml | nroff -man |
less'. A typical entry in a Makefile or Makefile.am is:
manpage.1: manpage.sgml
docbook-to-man $< > $@
The docbook-to-man binary is found in the docbook-to-man package.
Please remember that if you create the nroff version in one of the
debian/rules file targets (such as build), you will need to include
docbook-to-man in your Build-Depends control field.
-->
<!-- Fill in your name for FIRSTNAME and SURNAME. -->
<!ENTITY dhfirstname "<firstname>EuGene</firstname>">
<!ENTITY dhsurname "<surname>Team</surname>">
<!-- Please adjust the date whenever revising the manpage. -->
<!ENTITY dhdate "<date>April 1, 2005</date>">
<!-- SECTION should be 1-8, maybe w/ subsection other parameters are
allowed: see man(7), man(1). -->
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>eugene@ossau.toulouse.inra.fr</email>">
<!ENTITY dhusername "Marie-Josee Cros">
<!ENTITY dhucpackage "<refentrytitle>INRA-EUGENE</refentrytitle>">
<!ENTITY dhpackage "inra-eugene">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
]>
<refentry>
<refentryinfo>
<address>
&dhemail;
</address>
<author>
&dhfirstname;
&dhsurname;
</author>
<copyright>
<year>2003</year>
<holder>&dhusername;</holder>
</copyright>
&dhdate;
</refentryinfo>
<refmeta>
&dhucpackage;
&dhsection;
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose>A gene finder for Eukaryotics</refpurpose>
</refnamediv>
<refsect1>
<title>DESCRIPTION</title>
<para>This manual page was written for the &debian; distribution
because the original program does not have a manual page.</para>
<para><command>&dhpackage;</command> eugene is an open gene finder for eukaryotic organisms.</para>
</refsect1>
<refsect1>
<title>SEE ALSO</title>
<para>eugene (1).</para>
</refsect1>
<refsect1>
<title>AUTHOR</title>
<para>This manual page was written by &dhusername; &dhemail; for
the &debian; system (but may be used by others). Permission is
granted to copy, distribute and/or modify this document under
the terms of the &gnu; General Public License, Version 2 any
later version published by the Free Software Foundation.
</para>
<para>
On Debian systems, the complete text of the GNU General Public
License can be found in /usr/share/common-licenses/GPL.
</para>
</refsect1>
</refentry>
<!-- Keep this comment at the end of the file
Local variables:
mode: sgml
sgml-omittag:t
sgml-shorttag:t
sgml-minimize-attributes:nil
sgml-always-quote-attributes:t
sgml-indent-step:2
sgml-indent-data:t
sgml-parent-document:nil
sgml-default-dtd-file:nil
sgml-exposed-tags:nil
sgml-local-catalogs:nil
sgml-local-ecat-files:nil
End:
-->
#!/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 ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
config.status: configure
dh_testdir
# Add here commands to configure the package.
./configure --host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info
build: build-stamp
build-stamp: config.status
dh_testdir
# Add here commands to compile the package.
$(MAKE)
docbook-to-man debian/eugene.sgml |gzip -9 > debian/eugene.1.gz
docbook-to-man debian/egn_TrainIMM.sgml |gzip -9 > debian/egn_TrainIMM.1.gz
docbook-to-man debian/egn_WAMbuilder.sgml |gzip -9 > debian/egn_WAMbuilder.1.gz
docbook-to-man debian/egn_buildMarkovProt.sgml |gzip -9 > debian/egn_buildMarkovProt.1.gz
touch build-stamp
clean:
dh_testdir
dh_testroot
rm -f build-stamp
# Add here commands to clean up after the build process.
-$(MAKE) distclean
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
dh_clean
install: build
dh_testdir
dh_testroot
dh_clean -k
dh_installdirs
# Add here commands to install the package into debian/inra-eugene.
$(MAKE) install DESTDIR=$(CURDIR)/debian/inra-eugene
# 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
$(MAKE) install DESTDIR=$(CURDIR)/debian/tmp
install -d $(CURDIR)/debian/tmp/usr/share/man/man1