[med-svn] r5175 - trunk/packages/ensembl/ensembl/57/debian

Fri Aug 20 19:59:00 UTC 2010

Author: holland-guest
Date: 2010-08-20 19:58:59 +0000 (Fri, 20 Aug 2010)
New Revision: 5175

Modified:
   trunk/packages/ensembl/ensembl/57/debian/README.Debian
   trunk/packages/ensembl/ensembl/57/debian/README.source
   trunk/packages/ensembl/ensembl/57/debian/control
Log:
Some further writing, fix of dependencies.


Modified: trunk/packages/ensembl/ensembl/57/debian/README.Debian
===================================================================

--- trunk/packages/ensembl/ensembl/57/debian/README.Debian	2010-08-20 18:52:26 UTC (rev 5174)
+++ trunk/packages/ensembl/ensembl/57/debian/README.Debian	2010-08-20 19:58:59 UTC (rev 5175)
@@ -1,8 +1,12 @@
 ensembl for Debian
 ------------------
 
-Apache modules enabled in postinst include perl, headers, expires and
-deflate. These do not get disabled again on uninstall.
+Ensembl does not come with an installer. It is installed with the
+mindset of the developer of the database, for whom any separation
+of code-development and code-usage is a nuisance. So, we are
+introducing this separation here, as an intrinsic part of the
+Debian packaging. The README.source file explains the consequences
+in more detail.
 
 The (current) focus of this packaging is a running local web site.
 The genomic data remains on the remote servers. And it was produced
@@ -10,4 +14,22 @@
 for now, to end somewhere, all the extra bits are left as they are
 upstream, i.e. no further paths adjusted than ultimately required.
 
+We appreciate feedback from the community on this package. Also,
+if you have ideas for what you can do with it, or about what is
+missing to become truly useful - in the cloud or with your local
+installation, then please tell us. It is this feedback that motivates
+us to share our routine with Ensembl in the first place.
+
+CAVEATS (and they are big caveats):
+
+ * Ensembl wants an httpd to its very own control. So we run
+   a second instance on port 8000, not an extension of the
+   regular apache2 that we let say "It works!" as usual.
+
+ * The Ensembl install depends on archaic versions of
+   - BioPerl (1.2.3)
+   - libwww-perl (5.808)
+   which renders a series of regular packages uninstallable.
+   Please seriously consider installing Debian in a chroot environment.
+
  -- Richard Holland <holland at eaglegenomics.com>  Fri, 20 Aug 2010 14:46:17 +0200

Modified: trunk/packages/ensembl/ensembl/57/debian/README.source
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/README.source	2010-08-20 18:52:26 UTC (rev 5174)
+++ trunk/packages/ensembl/ensembl/57/debian/README.source	2010-08-20 19:58:59 UTC (rev 5175)
@@ -1,9 +1,12 @@
 ensembl for Debian
 ------------------
 
-<this file describes information about the source package, see Debian policy
-manual section 4.14. You WILL either need to modify or delete this file>
+Upstream sources have been mostly untouched. Changes address
+ * apache module paths that differ from those of the typical
+   upstream developer's machine
+ * paths to the Perl binary
+ * database setup
 
-
-
-
+Depending on the nature of the change to upstream, its may
+be either implemented as a quilt patch in debian/patches
+or be performed in debian/rules.

Modified: trunk/packages/ensembl/ensembl/57/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/control	2010-08-20 18:52:26 UTC (rev 5174)
+++ trunk/packages/ensembl/ensembl/57/debian/control	2010-08-20 19:58:59 UTC (rev 5175)
@@ -1,27 +1,35 @@
 Source: ensembl
 Section: unknown
 Priority: extra
-Maintainer: Richard Holland <holland at eaglegenomics.com>
-Build-Depends: debhelper (>= 7.0.50~), apache2, csh, expat, libdb-dev, libexpat1-dev, libgd2-noxpm-dev, libgdbm-dev, libgtk2.0-dev, libmysqlclient15-dev, libperl-dev, libperl5.10, libreadline5-dev, msttcorefonts, mysql-client, perl, zlib1g-dev, acedb-other-dotter, libcgi-pm-perl, libcgi-ajax-perl, libcache-memcached-perl, libcgi-session-perl, libclass-dbi-sweet-perl, libclass-std-perl, libclass-std-utils-perl, libcompress-bzip2-perl, libfile-spec-perl, libdata-uuid-libuuid-perl, libdb-file-lock-perl, libdbd-mysql, 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, libio-zlib-perl, libmime-types-perl, libmath-bezier-perl, librtf-writer-perl, libbio-das-lite-perl, bioperl1.2.3, libparallel-user-agent-perl
-Standards-Version: 3.8.4
-Homepage: <insert the upstream URL, if relevant>
-#Vcs-Git: git://git.debian.org/collab-maint/ensembl.git
-#Vcs-Browser: http://git.debian.org/?p=collab-maint/ensembl.git;a=summary
+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>
+DM-Upload-Allowed: yes
+Build-Depends: debhelper (>= 7.0.50~), mysql-client
+Standards-Version: 3.9.1.0
+Homepage: http://www.ensembl.org
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ensembl/ensembl/57/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ensembl/ensembl/57/
 
 Package: ensembl
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}, apache2, csh, expat,  msttcorefonts,  perl, acedb-other-dotter, libcgi-pm-perl, libcgi-ajax-perl, libcache-memcached-perl, libcgi-session-perl, libclass-dbi-sweet-perl, libclass-std-perl, libclass-std-utils-perl, libcompress-bzip2-perl, libfile-spec-perl, libdata-uuid-libuuid-perl, libdb-file-lock-perl, libdbd-mysql, 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, libio-zlib-perl, libmime-types-perl, libmath-bezier-perl, librtf-writer-perl, libbio-das-lite-perl, bioperl1.2.3, libparallel-user-agent-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. 
  .
- This is meant as an easy way to get a basic Ensembl installation working on 
- Debian. It can then be customised to local requirements.
+ This is meant as an easy way to get a basic Ensembl installation
+ working on Debian. It can then be customised to local requirements.
  . 
- Note that Ensembl has two odd dependencies: bioperl1.2.3 and libparallel-user-agent-perl. The former will conflict with any other existing bioperl installation and force you to downgrade. The latter will conflict with the latest libwww-perl installation and force a downgrade to 5.808, which will disable many other tools on your system. Therefore it is advisable NOT to install this package in parallel with any other software, and/or use a virtual machine or dedicated machine. 
+ Note that Ensembl has two odd dependencies: bioperl1.2.3 and
+ libparallel-user-agent-perl. The former will conflict with any
+ other existing bioperl installation and force you to downgrade.
+ The latter will conflict with the latest libwww-perl installation
+ and force a downgrade to 5.808, which will disable many other tools
+ on your system. Therefore it is advisable NOT to install this
+ package in parallel with any other software, and/or use a virtual
+ machine or dedicated machine.
  .
- We will work to try and remove these dependencies and allow Ensembl to run on an up-do-date machine.
- . 
- Note also that Ensembl completely takes over the Apache instance that runs it. Therefore you cannot serve any other sites from the same port number as Ensembl is using. You either have to shutdown your existing Apache on port 80, or assign Ensembl a different port number.
+ We will work to try and remove these dependencies and allow Ensembl
+ to run on an up-do-date machine.


