[med-svn] r5199 - trunk/packages/ensembl/ensembl/57/debian
Steffen Möller
moeller at alioth.debian.org
Sun Aug 29 22:39:00 UTC 2010
Author: moeller
Date: 2010-08-29 22:38:52 +0000 (Sun, 29 Aug 2010)
New Revision: 5199
Modified:
trunk/packages/ensembl/ensembl/57/debian/changelog
trunk/packages/ensembl/ensembl/57/debian/control
trunk/packages/ensembl/ensembl/57/debian/copyright
trunk/packages/ensembl/ensembl/57/debian/rules
Log:
Further split of packages.
Modified: trunk/packages/ensembl/ensembl/57/debian/changelog
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/changelog 2010-08-29 14:55:22 UTC (rev 5198)
+++ trunk/packages/ensembl/ensembl/57/debian/changelog 2010-08-29 22:38:52 UTC (rev 5199)
@@ -1,5 +1,11 @@
-ensembl (57-1) unstable; urgency=low
+ensembl (57-2) UNRELEASED; urgency=low
+ * Split packaging in many smaller packages (Closes: #589818)
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 29 Aug 2010 19:44:09 +0200
+
+ensembl (57-1) UNRELEASED; urgency=low
+
* Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
-- Richard Holland <holland at eaglegenomics.com> Fri, 20 Aug 2010 14:46:17 +0200
Modified: trunk/packages/ensembl/ensembl/57/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/control 2010-08-29 14:55:22 UTC (rev 5198)
+++ trunk/packages/ensembl/ensembl/57/debian/control 2010-08-29 22:38:52 UTC (rev 5199)
@@ -12,14 +12,23 @@
Package: ensembl
Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}, apache2, csh, expat, perl, libcgi-pm-perl, libcgi-session-perl, libdb-file-lock-perl, libdbd-mysql, perl-modules, mysql-server, ensembl-bin
+Depends: ${shlibs:Depends}, ${misc:Depends}, apache2, csh, expat, perl, libcgi-pm-perl, libcgi-session-perl, libdb-file-lock-perl, libdbd-mysql, perl-modules, mysql-server, ensembl-bin,libensembl-core-perl,libensembl-functgenomics-perl,libensembl-compara-perl,libensembl-external-perl,libensembl-variation-perl
Recommends: ttf-mscorefonts-installer, acedb-other-dotter, libcgi-ajax-perl, libcache-memcached-perl, libclass-dbi-sweet-perl, libclass-std-perl, libclass-std-utils-perl, libcompress-bzip2-perl, libfile-spec-perl, libdata-uuid-libuuid-perl, libgd-text-perl, libhash-merge-perl, libhtml-parser-perl, liblist-moreutils-perl, liblog-log4perl-perl, libmailtools-perl, libwww-curl-perl, libapache2-mod-perl2, libnumber-format-perl, libgd-gd2-noxpm-perl, libpdf-api2-perl, libsys-hostname-long-perl, libtemplate-plugin-number-format-perl, libxml-dom-perl, libxml-rss-perl, libxml-simple-perl, libbsd-resource-perl, libxml-xpath-perl, libxml-atom-perl, libjson-perl, libclass-data-inheritable-perl, libconfig-inifiles-perl, libdevel-stacktrace-perl, libexception-class-perl, libhtml-template-perl, libimage-size-perl, libio-string-perl, libipc-run-perl, libxml-libxml-perl, libole-storage-lite-perl, libparse-recdescent-perl, libspreadsheet-writeexcel-perl, libmime-types-perl, libmath-bezier-perl, librtf-writer-perl, libbio-das-lite-perl, bioperl1.2.3, libparallel-useragent-perl
Description: Installs a basic Ensembl 57 genome browser.
- The Ensembl 57 basic installation is a full copy of the public Ensembl
- website, minus Blast and SSAHA, and minus BioMart. It uses UniSearch instead
- of the engine used on the public site for searching by keyword. It connects
- directly to the public databases hosted by the EBI/Sanger.
+ Ensembl is a joint project of the Sanger Center and the European
+ Bioinformatics Institute, an outstation of the European Molecular
+ Biology Laboratory, (EMBL-EBI) that are sharing a campus in Hinxton
+ near Cambridge, UK. It presents the sequence data for the
+ yet available complete genomes of many vertebrates and is helped
+ by many sister-projects to cover also plants, invertebrates
+ and bacteria.
.
+ This package provides a basic installation of Ensembl. It comprises
+ a full copy of the public Ensembl website, minus Blast and SSAHA,
+ and minus BioMart. It uses UniSearch instead of the engine used on the
+ public site for searching by keyword. It connects directly to the public
+ databases hosted by the EBI/Sanger.
+ .
This is meant as an easy way to get a basic Ensembl installation
working on Debian. It can then be customised to local requirements.
.
@@ -35,6 +44,82 @@
We will work to try and remove these dependencies and allow Ensembl
to run on an up-do-date machine.
+Package: libensembl-core-perl
+Architecture: all
+Depends: bioperl1.2.3|bioperl
+Description: core libraries of Ensembl API
+ The Ensembl project presents the sequence data for the yet
+ available complete genomes of many vertebrates and is helped by many
+ sister-projects to cover also plants, invertebrates and bacteria.
+ .
+ This package provides the core of its API, defining basic concepts
+ like biological sequences and that there may be databases from
+ which information can be retrieved. If you work with the Ensembl
+ API, then you need this package.
+ .
+ For complete confidence in the functionality of your Ensembl
+ installation, version 1.2.3 of BioPerl should be used. There are
+ reports that a current version would also be functional, but
+ upstream thinks differently here.
+
+Package: libensembl-functgenomics-perl
+Depends: libensembl-core-perl
+Architecture: all
+Description: API for functional genomics with Ensembl
+ The Ensembl project presents the sequence data for the yet
+ available complete genomes of many vertebrates and is helped by many
+ sister-projects to cover also plants, invertebrates and bacteria.
+ .
+ Functional genomics is about the investigation of what effects
+ certain parts of the genome have across tissues, states of those
+ tissues (like hypoxia, temperature changes, growth, ...) and
+ of course in diseases.
+
+Package: libensembl-compara-perl
+Depends: libensembl-core-perl
+Architecture: all
+Description: API for comparative genomics with Ensembl
+ The Ensembl project presents the sequence data for the yet
+ available complete genomes of many vertebrates and is helped by many
+ sister-projects to cover also plants, invertebrates and bacteria.
+ .
+ Any creationist please ignore this package, it will not make any sense
+ to you. The others will see how genes known in the human can be traced
+ back down to the fly (and some developmental genes have for instance
+ even been proven to be functional in the fly), or that many genes have
+ kept their chromosomal vicinity over millions of years and yet some
+ nucleotides as a block remain unchanged while many other neighbouring
+ positions have undergone many changes .... maybe those that have not
+ changed mean something?
+
+Package: libensembl-external-perl
+Depends: libensembl-core-perl
+Architecture: all
+Description: API for integration of external data sources with Ensembl
+ The Ensembl project presents the sequence data for the yet
+ available complete genomes of many vertebrates and is helped by many
+ sister-projects to cover also plants, invertebrates and bacteria.
+ .
+ In a way, this package is the one that is most important for Debian,
+ since the integration of previous local data is (besides educational
+ purposes) probably the main motivation for the installation of these
+ pacakges.
+
+Package: libensembl-variation-perl
+Depends: libensembl-core-perl
+Architecture: all
+Description: Ensembl API for investigation of inter-individual genomic differences
+ The Ensembl project presents the sequence data for the yet
+ available complete genomes of many vertebrates and is helped by many
+ sister-projects to cover also plants, invertebrates and bacteria.
+ .
+ We humans don't have all the same DNA. We have come to accept that
+ as part of the problem in organ transplantation. Key of genetic research
+ is to link variants in the DNA with phenotypes. Of those, insights
+ in the molecular pathophysiology are preferred results since those
+ are likely to help a better understanding of current treatments
+ and may generate ideas for novel drugs at best.
+
Package: ensembl-bin
Architecture: any
Description: platform-specific files of Ensembl
Modified: trunk/packages/ensembl/ensembl/57/debian/copyright
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/copyright 2010-08-29 14:55:22 UTC (rev 5198)
+++ trunk/packages/ensembl/ensembl/57/debian/copyright 2010-08-29 22:38:52 UTC (rev 5199)
@@ -12,19 +12,16 @@
Upstream Author(s):
- <put author's name and email here>
- <likewise for another author>
+ Ewan Birney <birney at ebi.ac.uk>
+ and many others
Copyright:
- <Copyright (C) YYYY Firstname Lastname>
- <likewise for another author>
-
-License:
-
Copyright © 1999-2009 The European Bioinformatics Institute and
Genome Research Limited, and others. All rights reserved.
+License:
+
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
Modified: trunk/packages/ensembl/ensembl/57/debian/rules
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/rules 2010-08-29 14:55:22 UTC (rev 5198)
+++ trunk/packages/ensembl/ensembl/57/debian/rules 2010-08-29 22:38:52 UTC (rev 5199)
@@ -27,6 +27,8 @@
cp debian/ensembl.overwrites/Plugins.pm* $(DESTDIR)/usr/share/ensembl/conf/
cp debian/ensembl.overwrites/confSiteDefs.pm $(DESTDIR)/usr/share/ensembl/conf/SiteDefs.pm
cp debian/ensembl.overwrites/pluginSiteDefs.pm $(DESTDIR)/usr/share/ensembl/public-plugins/mirror/conf/SiteDefs.pm
+ # well, those should not have remained in the source tree in the first place, but, who knows...
+ find debian -name CVS -a -type d | xargs -r -rm -r
install-copying:
dh_testdir
@@ -37,10 +39,12 @@
echo "Creating directory '$$d'." ; \
mkdir -p "$$d" ; \
fi ; \
- cp -r conf ctrl_scripts ensembl ensembl-compara \
- ensembl-draw ensembl-external \
+ echo "Copying to '$$d'"; \
+ cp -r conf ctrl_scripts \
+ htdocs modules perl public-plugins utils \
+ ensembl ensembl-compara \
+ ensembl-external \
ensembl-functgenomics ensembl-variation \
- htdocs modules perl public-plugins utils \
$$d ; \
dd="$(DESTDIR)-bin/usr/bin" ; \
if [ ! -d "$$$d" ]; then \
@@ -48,16 +52,28 @@
mkdir -p "$$dd" ; \
fi ; \
mv $$d/ensembl-variation/C_code/calc_genotypes $$dd ; \
- ddd="$(DESTDIR)-doc/usr/share/doc/ensembl" ; \
- cd $$d; \
- for dddd in */docs ; \
- do \
- ddddd=`dirname $$dddd` ; \
- dddddd="$$ddd/usr/$$ddddd" ; \
- echo "moving documentation from $$dddd to $$dddddd" ; \
- mkdir -p "$$dddddd" ; \
- mv $$dddd/* $$dddddd/ ; \
+ ddd="$(DESTDIR)-doc/usr/share/doc/ensembl"
+
+ m="$(DESTDIR)-doc/usr/share/doc/ensembl-doc"; if [ ! -d "$$m" ]; then mkdir -p "$$m"; fi ; \
+ for doc in $(DESTDIR)/usr/share/ensembl/*/docs ; do \
+ docdir=`dirname $$doc` ; \
+ docdirbase=`basename $$docdir` ; \
+ mv $(DESTDIR)/usr/share/ensembl/$$docdirbase/docs $$m/$$docdirbase ; \
done
+
+ for p in core compara external functgenomics variation; do \
+ destdir="$(CURDIR)/debian/libensembl-$${p}-perl/usr/share/ensembl" ; \
+ if [ ! -d "$$destdir" ]; then mkdir -p "$$destdir"; fi ; \
+ done
+
+ mv $(CURDIR)/debian/ensembl/usr/share/ensembl/ensembl $(CURDIR)/debian/libensembl-core-perl/usr/share/ensembl
+ sourcedir="$(CURDIR)/debian/ensembl/usr/share/ensembl" ; \
+ for p in compara external functgenomics variation; do \
+ destdir="$(CURDIR)/debian/libensembl-$${p}-perl/usr/share/ensembl" ; \
+ echo "Moving '$$sourcedir/*-$$p' to '$$destdir'" ; \
+ mv $${sourcedir}/*-$$p $$destdir ; \
+ done
+
touch $@
install-paths: install-copying
@@ -84,6 +100,7 @@
dh_install
dh_installman
dh_installinit
+ dh_link
dh_strip
dh_compress
dh_fixperms
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