[med-svn] r5945 - trunk/packages/ensembl/ensembl/57/debian
Steffen Möller
moeller at alioth.debian.org
Thu Feb 10 15:37:53 UTC 2011
Author: moeller
Date: 2011-02-10 15:37:52 +0000 (Thu, 10 Feb 2011)
New Revision: 5945
Modified:
trunk/packages/ensembl/ensembl/57/debian/README.Debian
trunk/packages/ensembl/ensembl/57/debian/README.source
trunk/packages/ensembl/ensembl/57/debian/changelog
trunk/packages/ensembl/ensembl/57/debian/control
Log:
Moving Ensembl to non-free.
Modified: trunk/packages/ensembl/ensembl/57/debian/README.Debian
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/README.Debian 2011-02-10 15:29:02 UTC (rev 5944)
+++ trunk/packages/ensembl/ensembl/57/debian/README.Debian 2011-02-10 15:37:52 UTC (rev 5945)
@@ -42,5 +42,10 @@
* Installation (first startup) will take 1-2 hours to download the
Ensembl meta-data from the Sanger/EBI servers.
+
+Non-free - not really. Ensembl is free, but is ships with the
+.jar file of jalview that we for the moment cannot offer as a
+Debian package.
+
-- Richard Holland <holland at eaglegenomics.com> Fri, 20 Aug 2010 14:46:17 +0200
Steffen Moeller <moeller at debian.org> Sat, 30 Oct 2010 22:29:05 +0200
Modified: trunk/packages/ensembl/ensembl/57/debian/README.source
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/README.source 2011-02-10 15:29:02 UTC (rev 5944)
+++ trunk/packages/ensembl/ensembl/57/debian/README.source 2011-02-10 15:37:52 UTC (rev 5945)
@@ -6,6 +6,9 @@
upstream developer's machine
* paths to the Perl binary
* database setup
+and for DFSG compliance
+ * Removal of PDFs
+ * Removal of jar (of Ensembl internal nature)
Depending on the nature of the change to upstream, its may
be either implemented as a quilt patch in debian/patches
@@ -15,3 +18,43 @@
upstream CVS repository. The script
prepare_ensembl_source_packages.sh
guides through this process.
+
+
+Concerning the removal of PDFs, the following files were
+affected:
+
+./ensembl-57/htdocs/info/website/tutorials/module4_feb2009_ensembl.pdf
+./ensembl-57/htdocs/info/website/tutorials/module2_feb2009_ensembl.pdf
+./ensembl-57/htdocs/info/website/tutorials/module3_feb2009_ensembl.pdf
+./ensembl-57/htdocs/info/website/tutorials/coursebook.pdf
+./ensembl-57/htdocs/info/website/tutorials/Ensembl_introduction.pdf
+./ensembl-57/htdocs/info/website/tutorials/variations_worked_example.pdf
+./ensembl-57/htdocs/info/website/tutorials/module1_feb2009_ensembl.pdf
+./ensembl-57/htdocs/info/website/tutorials/mining_with_biomart.pdf
+./ensembl-57/htdocs/info/website/tutorials/biomart_linked_dataset.pdf
+./ensembl-57/htdocs/info/website/tutorials/module5_feb2009_ensembl.pdf
+./ensembl-57/htdocs/info/website/tutorials/biomart_worked_ex.pdf
+./ensembl-57/htdocs/info/docs/api/variation/variation-database-schema.pdf
+./ensembl-57/htdocs/info/docs/das/LDAS_setup.pdf
+./ensembl-57/htdocs/info/docs/das/proserver_installation.pdf
+./ensembl-57/htdocs/info/docs/das/CSS_support.pdf
+./ensembl-57/htdocs/info/docs/das/proserver-guide.pdf
+./ensembl-57/htdocs/info/docs/das/DASTalk.pdf
+./ensembl-57/htdocs/info/docs/das/EnsemblUploadFormatV2.pdf
+./ensembl-57/ensembl/docs/tutorial/ensembl_tutorial.pdf
+./ensembl-57/ensembl/docs/ensembl_das/ensembl-das.pdf
+./ensembl-57/ensembl/misc-scripts/xref_mapping/ensembl_xrefs.pdf
+./ensembl-57/ensembl-variation/schema/database-schema.pdf
+./ensembl-57/ensembl-variation/schema/database-schema-print.pdf
+./ensembl-57/public-plugins/ensembl/htdocs/info/about/legal/Ensembl_mirror_policy_v1.pdf
+./ensembl-57/public-plugins/ensembl/htdocs/info/about/legal/Ensembl_logo_policy_v1.pdf
+./ensembl-57/public-plugins/ensembl/htdocs/Anopheles_gambiae/documents/press.pdf
+
+Alone the ComparaTutorial comes with a MS Word .doc file,
+that allows this to remain in the source tree.
+
+The BuildSynteny.jar file is removed from the source tree since it is
+binary. It does ship with the sources.
+
+The jalview sources are not redistributed. The dependency on the jalview
+.jar renders the Ensembl package non-free for the time speaking.
Modified: trunk/packages/ensembl/ensembl/57/debian/changelog
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/changelog 2011-02-10 15:29:02 UTC (rev 5944)
+++ trunk/packages/ensembl/ensembl/57/debian/changelog 2011-02-10 15:37:52 UTC (rev 5945)
@@ -1,11 +1,23 @@
-ensembl (57-5) experimental; urgency=low
+ensembl (57-6) experimental; urgency=low
+ * Yet another revised upload (Closes: #589818).
+ - removal of PDFs from source tree
+ - removal of .jar
+ * Another jar (of jalview) cannot be removed for the moment and
+ thus remains and renders the package non-free. But we are working
+ on getting Jalview into the distrbution. This cannot take too
+ much longer.
+
+ -- Steffen Moeller <moeller at debian.org> Thu, 10 Feb 2011 16:37:34 +0100
+
+ensembl (57-5) UNRELEASED; urgency=low
+
* Finalising postinst.
- * Revised initial upload (Closes: #589818).
+ * Revised initial upload.
-- Richard Holland <holland at eaglegenomics.com> Tue, 01 Feb 2011 22:36:09 +0100
-ensembl (57-4) experimental; urgency=low
+ensembl (57-4) UNRELEASED; urgency=low
* Initial upload
* More steps towards lintian cleanliness.
Modified: trunk/packages/ensembl/ensembl/57/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/control 2011-02-10 15:29:02 UTC (rev 5944)
+++ trunk/packages/ensembl/ensembl/57/debian/control 2011-02-10 15:37:52 UTC (rev 5945)
@@ -1,5 +1,5 @@
Source: ensembl
-Section: science
+Section: non-free/science
Priority: extra
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Richard Holland <holland at eaglegenomics.com>, Steffen Moeller <moeller at debian.org>
@@ -16,7 +16,7 @@
Depends: ${shlibs:Depends}, ${misc:Depends}, apache2-mpm-prefork, csh, expat, perl, libcgi-pm-perl, libcgi-session-perl, libdb-file-lock-perl, libdbd-mysql, perl-modules, ensembl-bin, libensembl-core-perl,libensembl-functgenomics-perl,libensembl-compara-perl,libensembl-external-perl,libensembl-variation-perl, tcsh, liblwp-parallel-perl, mysql-server, mysql-client
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|bioperl
Suggests: ksh | mksh | pdksh | zsh
-Section: science
+Section: non-free/science
Description: Installs a basic Ensembl 57 genome browser.
Ensembl is a joint project of the Sanger Center and the European
Bioinformatics Institute, an outstation of the European Molecular
@@ -58,7 +58,7 @@
Architecture: all
Depends: ${misc:Depends},bioperl1.2.3|bioperl
Suggests: ksh | mksh | pdksh | zsh, tk
-Section: perl
+Section: non-free/perl
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
@@ -77,7 +77,7 @@
Package: libensembl-functgenomics-perl
Depends: ${misc:Depends},libensembl-core-perl
Architecture: all
-Section: perl
+Section: non-free/perl
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
@@ -90,7 +90,7 @@
Package: libensembl-compara-perl
Depends: ${misc:Depends},libensembl-core-perl
Architecture: all
-Section: perl
+Section: non-free/perl
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
@@ -108,7 +108,7 @@
Package: libensembl-external-perl
Depends: ${misc:Depends},libensembl-core-perl
Architecture: all
-Section: perl
+Section: non-free/perl
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
@@ -122,7 +122,7 @@
Package: libensembl-variation-perl
Depends: ${misc:Depends},libensembl-core-perl
Architecture: all
-Section: perl
+Section: non-free/perl
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
@@ -138,7 +138,7 @@
Package: libensembl-draw-perl
Depends: ${misc:Depends},libensembl-core-perl
Architecture: all
-Section: perl
+Section: non-free/perl
Description: Ensembl API for graphical representation of genomic properties
The Ensembl project presents the sequence data for the yet
available complete genomes of many vertebrates and is helped by many
@@ -150,14 +150,14 @@
Package: ensembl-bin
Depends: ${shlibs:Depends}, ${misc:Depends}
Architecture: any
-Section: utils
+Section: non-free/utils
Description: platform-specific files of Ensembl
The Ensembl website is mostly implemented in Perl. But just a few
bits do appear as binaries. Those are gathered in this package.
Package: ensembl-doc
Depends: ${misc:Depends}
-Section: doc
+Section: non-free/doc
Architecture: all
Description: tutorials and othe documentation for Ensembl
Several Perl packages of Ensmebl offer a description of their API.
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