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 <[email protected]> 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 <[email protected]> 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 <[email protected]> + 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
