[med-svn] r5205 - trunk/packages/ensembl/ensembl/57/debian

[Steffen Möller]

Author: moeller
Date: 2010-08-31 10:08:29 +0000 (Tue, 31 Aug 2010)
New Revision: 5205

Modified:
   trunk/packages/ensembl/ensembl/57/debian/control
   trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs
Log:
bioperl may substitute bioperl1.2.3


Modified: trunk/packages/ensembl/ensembl/57/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/control	2010-08-30 21:34:08 UTC (rev 5204)
+++ trunk/packages/ensembl/ensembl/57/debian/control	2010-08-31 10:08:29 UTC (rev 5205)
@@ -12,8 +12,9 @@
 
 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,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
+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, 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|bioperl
+Suggests: libparallel-useragent-perl
 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
@@ -33,16 +34,20 @@
  working on Debian. It can then be customised to local requirements.
  . 
  Note that Ensembl has two odd dependencies: bioperl1.2.3 and
- libparallel-useragent-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
+ libparallel-useragent-perl. Those are not required for routine
+ browsing, but the bioperl1.2.3 library performs the parsing
+ of BLAST outputs. Version 1.2.3 is in conflict with any
+ other existing bioperl installation and force you to effectively
+ downgrade.
+ .
+ libwww-perl5.808  will conflict with the latest libwww-perl installation
+ and thus 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.
+ to run fully on an up-do-date machine.
 
 Package: libensembl-core-perl
 Architecture: all

Modified: trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs	2010-08-30 21:34:08 UTC (rev 5204)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.dirs	2010-08-31 10:08:29 UTC (rev 5205)
@@ -1,6 +1,11 @@
-usr/bin
+var
 var/log
+var/log/ensembl
+var/log
 usr/share/ensembl/logs
+var/cache
+var/cache/ensembl
 var/cache/ensembl/img-cache
+var/tmp/ensembl
 var/tmp/ensembl/img-tmp
 var/tmp/ensembl/tmp