[med-svn] r9108 - in trunk/packages/ensembl/ensembl/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2011-12-26 23:18:36 +0000 (Mon, 26 Dec 2011)
New Revision: 9108

Modified:
   trunk/packages/ensembl/ensembl/trunk/debian/changelog
   trunk/packages/ensembl/ensembl/trunk/debian/control
   trunk/packages/ensembl/ensembl/trunk/debian/init.d
   trunk/packages/ensembl/ensembl/trunk/debian/patches/use_ksh_only_if_needed.patch
Log:
Work on some lintian warnings regarding documentation issues


Modified: trunk/packages/ensembl/ensembl/trunk/debian/changelog
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/changelog	2011-12-26 15:18:22 UTC (rev 9107)
+++ trunk/packages/ensembl/ensembl/trunk/debian/changelog	2011-12-26 23:18:36 UTC (rev 9108)
@@ -15,6 +15,8 @@
     - no need for ${shlibs:Depends} in ensembl (arch=all)
     - libensembl-core-perl Depends: ksh | mksh | pdksh | zsh
       because this package really contains such scripts
+    - remove duplicated section entries
+    - slightly enhanced long descriptions
   * debian/prepare_ensembl_source_packages.sh:
     - Make sure the files that should be removed will be really removed
     - Make script way less noisy
@@ -64,9 +66,7 @@
     csh is not tested).  Because csh-considered-harmful we do not like
     to advertise csh for no need at all and the patch is just dropping
     csh references.
-  * debian/patches/use_ksh_only_if_needed.patch: convert last remaining
-    script in ensembl that uses ksh to bash to get rid of useless
-    dependency
+  * debian/init.d: Added description
 
  -- Andreas Tille <tille at debian.org>  Thu, 15 Dec 2011 19:01:29 +0100
 

Modified: trunk/packages/ensembl/ensembl/trunk/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/control	2011-12-26 15:18:22 UTC (rev 9107)
+++ trunk/packages/ensembl/ensembl/trunk/debian/control	2011-12-26 23:18:36 UTC (rev 9108)
@@ -41,7 +41,6 @@
  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
-Section: non-free/science
 Description: basic Ensembl genome browser
  Ensembl is a joint project of the Sanger Center and the European
  Bioinformatics Institute, an outstation of the European Molecular
@@ -72,9 +71,6 @@
  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 fully on an up-do-date machine.
- .
  WARNING: Requires internet connection both to install and to run, as it
  connects to the Sanger/EBI database servers during both installation 
  and at runtime.
@@ -149,16 +145,15 @@
 Architecture: all
 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
+ 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.
+ Humans don't have all the same DNA.  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: libensembl-draw-perl
 Depends: ${misc:Depends}, libensembl-core-perl (= ${source:Version})
@@ -175,7 +170,6 @@
 Package: ensembl-bin
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Architecture: any
-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.

Modified: trunk/packages/ensembl/ensembl/trunk/debian/init.d
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/init.d	2011-12-26 15:18:22 UTC (rev 9107)
+++ trunk/packages/ensembl/ensembl/trunk/debian/init.d	2011-12-26 23:18:36 UTC (rev 9108)
@@ -7,6 +7,13 @@
 # Default-Stop:      0 1 6
 # X-Interactive:     true
 # Short-Description: Start/stop ensembl web server
+# Description:       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.
 ### END INIT INFO
 
 set -e

Modified: trunk/packages/ensembl/ensembl/trunk/debian/patches/use_ksh_only_if_needed.patch
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/patches/use_ksh_only_if_needed.patch	2011-12-26 15:18:22 UTC (rev 9107)
+++ trunk/packages/ensembl/ensembl/trunk/debian/patches/use_ksh_only_if_needed.patch	2011-12-26 23:18:36 UTC (rev 9108)
@@ -1,3 +1,11 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Thu, 15 Dec 2011 19:01:29 +0100
+Description: Try to avoid usage of ksh
+ There is one script with .sh extension in the ensembl binary package
+ which finally does not really need ksh if we replace print statements
+ by echo statements which is finally worth the patch to avoid an
+ unneeded dependency.
+
 --- ensembl-65.orig/utils/server_maintenance/cvs_update_web_only.sh
 +++ ensembl-65/utils/server_maintenance/cvs_update_web_only.sh
 @@ -1,4 +1,4 @@