[med-svn] r14715 - in trunk/packages/emboss-explorer/tags: . 2.2.0-8/debian 2.2.0-8/debian/patches
Charles Plessy
plessy at alioth.debian.org
Sun Sep 15 05:08:16 UTC 2013
Author: plessy
Date: 2013-09-15 05:08:14 +0000 (Sun, 15 Sep 2013)
New Revision: 14715
Added:
trunk/packages/emboss-explorer/tags/2.2.0-8/
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/changelog
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/compat
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/control
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.apache2
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.apache2.conf
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.desktop
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.install
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.links
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.lintian-overrides
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/index.html
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/01-fix_examples.diff
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/02-fix_Conf.pm.diff
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/05-build-manpages.diff
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/emboss-6.4-group-list.patch
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/series
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/rules
Removed:
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/apache.conf
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/changelog
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/compat
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/control
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.desktop
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.install
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.links
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.postinst
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.postrm
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/index.html
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/01-fix_examples.diff
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/02-fix_Conf.pm.diff
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/05-build-manpages.diff
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/series
trunk/packages/emboss-explorer/tags/2.2.0-8/debian/rules
Log:
[svn-buildpackage] Tagging emboss-explorer 2.2.0-8
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/apache.conf
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/apache.conf 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/apache.conf 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,22 +0,0 @@
-# I used /etc/gallery2/apache.conf as a template. -- Charles Plessy
-Alias /emboss-explorer /usr/share/emboss-explorer/html
-
-<Directory /usr/share/emboss-explorer/html>
- Options FollowSymLinks
-# AllowOverride Limit Options FileInfo
-</Directory>
-
-Alias /doc/emboss-explorer/ "/usr/share/doc/emboss-explorer/"
-<Directory "/usr/share/doc/emboss-explorer/">
- Options Indexes MultiViews FollowSymLinks
- AllowOverride None
- Order allow,deny
- Allow from all
-</Directory>
-
-# some people prefer a simple URL like http://emboss-explorer.example
-#<VirtualHost 1.2.3.4>
-# DocumentRoot /usr/share/emboss-explorer
-# ServerName emboss-explorer.example
-#</VirtualHost>
-
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/changelog
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/changelog 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/changelog 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,143 +0,0 @@
-emboss-explorer (2.2.0-8) UNRELEASED; urgency=low
-
- [ David Paleino ]
- * Removed myself from Uploaders
-
- [ Charles Plessy ]
- * Converted patches from dpatch to quilt format.
- * Converted the source package to dpkg source format 3.0 (quilt).
- * Added a DEP 3 header to the patches.
- * Removed debian/emboss-explorer.preinst, useless after Lenny.
- * Conforms with Policy 3.9.2 (debian/control, no other changes needed).
- * Corrected VCS URLs in debian/control.
- * Updated debian/copyright to latest machine-readable format.
- * Switch to Debhelpers compatibility level 8 (debian/compat, debian/control).
- * Convert to Debhelper's tiny mode (debian/rules, debian/docs).
-
- -- David Paleino <d.paleino at gmail.com> Sat, 23 May 2009 14:43:42 +0200
-
-emboss-explorer (2.2.0-7) unstable; urgency=low
-
- * debian/emboss-explorer.postinst: reloads apache.
- * debian/menu, debian/emboss-explorer.desktop,
- debian/rules, debian/emboss-explorer.install: adding menu entries starting
- a browser on http://localhost/emboss-explorer.
- * debian/README.source, debian/control: added instructions for patching
- and updated Standards-Version.
- * debian/compat, debian/control: using Debhelper 7.
-
- -- Charles Plessy <plessy at debian.org> Sun, 07 Dec 2008 20:21:35 +0900
-
-emboss-explorer (2.2.0-6) unstable; urgency=low
-
- [ Charles Plessy ]
- * Relicensed the packaging work to "Same as EMBOSS explorer".
- * debian/patches:
- - Documented 01-fix_examples.dpatch.
- - Documented and forwarded 02-fix_Conf.pm.dpatch and
- 05-build-manpages.dpatch.
- - Suppressed 04-fix_install.dpatch. Its role is taken by debian/rules and
- debian/index.html.
- * debian/rules:
- - refreshed using dh-make-perl version 0.45;
- - tests disable because of upstream bug 1994385;
- - sets the owner of the emboss output directory as `www-data';
- - touches the makefile to avoid timestamp artefacts due to the patching of
- Makefile.PL (Thanks to Damyan and Gregor for the hint!).
- * Package made compatible with FHS by not using /var/www.
- - HTML files moved to `/usr/emboss-explorer/html'.
- - Cascade stylesheets moved to `/etc/emboss-explorer/style'
- (they are intended to be modifiable).
- - Temporary files moved to `/var/lib/emboss-explorer'
- - /etc/emboss-explorer/apache.conf allows apache2 to access the files in
- the /user/share/emboss-explorer directory, as well as the EMBOSS
- documentation in /usr/share/doc/emboss-explorer/ (Closes: #485735).
- * debian/emboss-explorer.manpages, debian/acdcheck.1*, debian/mkstatic.1*
- suppressed to use Upstream's manpages.
- * debian/emboss-explorer.postrm removes the temporary files when the package
- is purged.
- * debian/emboss-explorer.preinst moves the emboss-explorer.conf in its new
- place.
-
- [ David Paleino ]
- * debian/control:
- - dropped dependency on libcgi-perl (Closes: #485009)
- - updated Charles' email :)
- * debian/copyright updated
-
- -- Charles Plessy <plessy at debian.org> Sat, 05 Jul 2008 16:29:07 +0900
-
-emboss-explorer (2.2.0-5) unstable; urgency=low
-
- * debian/control:
- - Allowed upload by Debian maintainers.
- - Changed Maintainer to Debian-Med Packaging Team.
- - Changed VCS to Debian-Med's subversion repository.
- - Checked conformance with Policy 3.7.3 (no changes needed).
- * debian/copyright: converted to machine-readable format.
-
- -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 05 Mar 2008 20:14:55 +0900
-
-emboss-explorer (2.2.0-4) unstable; urgency=low
-
- [ David Paleino ]
- * debian/do_cleanup.sh removed -- its contents are now directly
- put in the crontab file. (Closes: #435991)
-
- [ Charles Plessy ]
- * Gave ownersip of /var/www/emboss-explorer/output to www-data in
- debian/rules, removed the postinst script which was doing this before.
- * Added a reference to the stylesheets in the xml sources of the
- manpages, to simplify their use with xsltproc.
- * Generated the manpages offline, and dropped the build-dependency on
- xsltproc, docbook-xml and docbook-xsl.
- * Using debian/emboss-explorer instead of debian/tmp as build directory.
- * Removed the XS- prefix in front of the Vcs-* fields on debian/control.
- * Removed instructions to handle a deleted script, do_cleanup.sh
-
- -- Charles Plessy <charles-debian-nospam at plessy.org> Mon, 05 Nov 2007 10:38:07 +0900
-
-emboss-explorer (2.2.0-3) unstable; urgency=low
-
- [ David Paleino ]
- * debian/do_cleanup.sh added to handle crontab (Closes: #435991)
- * debian/emboss-explorer.cron.d and debian/emboss-explorer.install
- edited to reflect the changes
- * debian/emboss-explorer.dirs edited to add /usr/share/emboss-explorer/
- * debian/control - removing unused ${misc:Depends}
-
- [ Charles Plessy ]
- * Changed section of libemboss-acd-perl from science to perl.
-
- -- David Paleino <d.paleino at gmail.com> Sun, 07 Oct 2007 13:08:54 +0200
-
-emboss-explorer (2.2.0-2) unstable; urgency=low
-
- * Migration from /var/www/emboss to /var/www/emboss-explorer was
- incomplete. Correcting this.
- * Fixed double-building of the manpages.
- * Added myself to the uploaders.
- * Swiched to apache2 as the default webserver.
- * emboss-explorer.conf now defaults to /usr/lib/emboss, which is the
- only place where the emboss binaries are guaranteed to keep their
- original name (therefore depending on emboss >= 5.0.0).
- * Provides emboss-explorer.conf through a file, not a patch. Modifying
- ./install so that it does not manipulate emboss-explorer.conf anymore
- so that there is a single entry point to change the default
- configuration.
- * Added a configure rule so that the clean rule can always run make clean.
- * Using include /usr/share/dpatch/dpatch.make.
- * Added libcgi-perl in the Depends: field of emboss-explorer.
- * Added libparse-recdescent-perl in the Depends: field of
- libemboss-acd-perl (Thanks to Anthony Boureux).
- * Moved dpatch from Build-depends-indep to Build-depends, because it is
- needed for debian/rules clean.
-
- -- Charles Plessy <charles-debian-nospam at plessy.org> Sun, 15 Jul 2007 16:08:24 +0900
-
-emboss-explorer (2.2.0-1) experimental; urgency=low
-
- * Initial release (Closes: #423548)
-
- -- David Paleino <d.paleino at gmail.com> Sat, 12 May 2007 17:52:59 +0200
-
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/changelog (from rev 14714, trunk/packages/emboss-explorer/trunk/debian/changelog)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/changelog (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/changelog 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,162 @@
+emboss-explorer (2.2.0-8) unstable; urgency=low
+
+ [ David Paleino ]
+ * Removed myself from Uploaders
+
+ [ Charles Plessy ]
+ * Converted patches from dpatch to quilt format.
+ * Converted the source package to dpkg source format 3.0 (quilt).
+ * Added a DEP 3 header to the patches.
+ * Removed debian/emboss-explorer.preinst, useless after Lenny.
+ * Conforms with Policy 3.9.4 (debian/control, no other changes needed).
+ * Use canonical VCS URLs in debian/control.
+ * Updated debian/copyright to latest machine-readable format.
+ * Switch to Debhelpers compatibility level 9 (debian/compat, debian/control).
+ * Convert to Debhelper's tiny mode (debian/rules, debian/docs).
+ * Removed obsolete DM-Upload-Allowed field.
+ * Normalised debian/control with config-model-edit.
+ * Removed restriction on EMBOSS version, satisified even in oldstable.
+ * Verbose build logs (debian/rules).
+ * Added Debhelper’s misc:Depends substitution variable.
+ * Use dh_apache2 (Closes: #669738).
+ - Build-depend on apache2-dev for dh_apache2.
+ - Invoke dh_apache2 through dh.
+ - Updated Apache configuration file for 2.4.
+ - Updated debian/emboss-explorer.links for new name of configuration file.
+ - Override ‘apache2-deprecated-auth-config’ warning (would conflict
+ with another file).
+ - Delete obsolete postinst and postrm files.
+ - Recommend apache2 or httpd through misc:Recommends.
+ * Added keywords to the desktop entry.
+ * Correct path for moving ACD.pm and its manual page.
+ * Apply patch from upstream tracker to use emboss-explorer with EMBOSS 6.4
+ (Closes: #722982 LP:#1083426).
+ * Correct the alias to the EMBOSS documentation. Closes: #485735.
+
+ -- Charles Plessy <plessy at debian.org> Sun, 15 Sep 2013 13:50:12 +0900
+
+emboss-explorer (2.2.0-7) unstable; urgency=low
+
+ * debian/emboss-explorer.postinst: reloads apache.
+ * debian/menu, debian/emboss-explorer.desktop,
+ debian/rules, debian/emboss-explorer.install: adding menu entries starting
+ a browser on http://localhost/emboss-explorer.
+ * debian/README.source, debian/control: added instructions for patching
+ and updated Standards-Version.
+ * debian/compat, debian/control: using Debhelper 7.
+
+ -- Charles Plessy <plessy at debian.org> Sun, 07 Dec 2008 20:21:35 +0900
+
+emboss-explorer (2.2.0-6) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * Relicensed the packaging work to "Same as EMBOSS explorer".
+ * debian/patches:
+ - Documented 01-fix_examples.dpatch.
+ - Documented and forwarded 02-fix_Conf.pm.dpatch and
+ 05-build-manpages.dpatch.
+ - Suppressed 04-fix_install.dpatch. Its role is taken by debian/rules and
+ debian/index.html.
+ * debian/rules:
+ - refreshed using dh-make-perl version 0.45;
+ - tests disable because of upstream bug 1994385;
+ - sets the owner of the emboss output directory as `www-data';
+ - touches the makefile to avoid timestamp artefacts due to the patching of
+ Makefile.PL (Thanks to Damyan and Gregor for the hint!).
+ * Package made compatible with FHS by not using /var/www.
+ - HTML files moved to `/usr/emboss-explorer/html'.
+ - Cascade stylesheets moved to `/etc/emboss-explorer/style'
+ (they are intended to be modifiable).
+ - Temporary files moved to `/var/lib/emboss-explorer'
+ - /etc/emboss-explorer/apache.conf allows apache2 to access the files in
+ the /user/share/emboss-explorer directory, as well as the EMBOSS
+ documentation in /usr/share/doc/emboss-explorer/ (Closes: #485735).
+ * debian/emboss-explorer.manpages, debian/acdcheck.1*, debian/mkstatic.1*
+ suppressed to use Upstream's manpages.
+ * debian/emboss-explorer.postrm removes the temporary files when the package
+ is purged.
+ * debian/emboss-explorer.preinst moves the emboss-explorer.conf in its new
+ place.
+
+ [ David Paleino ]
+ * debian/control:
+ - dropped dependency on libcgi-perl (Closes: #485009)
+ - updated Charles' email :)
+ * debian/copyright updated
+
+ -- Charles Plessy <plessy at debian.org> Sat, 05 Jul 2008 16:29:07 +0900
+
+emboss-explorer (2.2.0-5) unstable; urgency=low
+
+ * debian/control:
+ - Allowed upload by Debian maintainers.
+ - Changed Maintainer to Debian-Med Packaging Team.
+ - Changed VCS to Debian-Med's subversion repository.
+ - Checked conformance with Policy 3.7.3 (no changes needed).
+ * debian/copyright: converted to machine-readable format.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 05 Mar 2008 20:14:55 +0900
+
+emboss-explorer (2.2.0-4) unstable; urgency=low
+
+ [ David Paleino ]
+ * debian/do_cleanup.sh removed -- its contents are now directly
+ put in the crontab file. (Closes: #435991)
+
+ [ Charles Plessy ]
+ * Gave ownersip of /var/www/emboss-explorer/output to www-data in
+ debian/rules, removed the postinst script which was doing this before.
+ * Added a reference to the stylesheets in the xml sources of the
+ manpages, to simplify their use with xsltproc.
+ * Generated the manpages offline, and dropped the build-dependency on
+ xsltproc, docbook-xml and docbook-xsl.
+ * Using debian/emboss-explorer instead of debian/tmp as build directory.
+ * Removed the XS- prefix in front of the Vcs-* fields on debian/control.
+ * Removed instructions to handle a deleted script, do_cleanup.sh
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Mon, 05 Nov 2007 10:38:07 +0900
+
+emboss-explorer (2.2.0-3) unstable; urgency=low
+
+ [ David Paleino ]
+ * debian/do_cleanup.sh added to handle crontab (Closes: #435991)
+ * debian/emboss-explorer.cron.d and debian/emboss-explorer.install
+ edited to reflect the changes
+ * debian/emboss-explorer.dirs edited to add /usr/share/emboss-explorer/
+ * debian/control - removing unused ${misc:Depends}
+
+ [ Charles Plessy ]
+ * Changed section of libemboss-acd-perl from science to perl.
+
+ -- David Paleino <d.paleino at gmail.com> Sun, 07 Oct 2007 13:08:54 +0200
+
+emboss-explorer (2.2.0-2) unstable; urgency=low
+
+ * Migration from /var/www/emboss to /var/www/emboss-explorer was
+ incomplete. Correcting this.
+ * Fixed double-building of the manpages.
+ * Added myself to the uploaders.
+ * Swiched to apache2 as the default webserver.
+ * emboss-explorer.conf now defaults to /usr/lib/emboss, which is the
+ only place where the emboss binaries are guaranteed to keep their
+ original name (therefore depending on emboss >= 5.0.0).
+ * Provides emboss-explorer.conf through a file, not a patch. Modifying
+ ./install so that it does not manipulate emboss-explorer.conf anymore
+ so that there is a single entry point to change the default
+ configuration.
+ * Added a configure rule so that the clean rule can always run make clean.
+ * Using include /usr/share/dpatch/dpatch.make.
+ * Added libcgi-perl in the Depends: field of emboss-explorer.
+ * Added libparse-recdescent-perl in the Depends: field of
+ libemboss-acd-perl (Thanks to Anthony Boureux).
+ * Moved dpatch from Build-depends-indep to Build-depends, because it is
+ needed for debian/rules clean.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sun, 15 Jul 2007 16:08:24 +0900
+
+emboss-explorer (2.2.0-1) experimental; urgency=low
+
+ * Initial release (Closes: #423548)
+
+ -- David Paleino <d.paleino at gmail.com> Sat, 12 May 2007 17:52:59 +0200
+
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/compat
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/compat 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/compat 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1 +0,0 @@
-8
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/compat (from rev 14686, trunk/packages/emboss-explorer/trunk/debian/compat)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/compat (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/compat 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1 @@
+9
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/control
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/control 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/control 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,38 +0,0 @@
-Source: emboss-explorer
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Charles Plessy <plessy at debian.org>
-Build-Depends: debhelper (>= 8)
-Build-Depends-Indep: libparse-recdescent-perl, libmailtools-perl
-Standards-Version: 3.9.2
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/emboss-explorer/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/emboss-explorer/trunk/
-Homepage: http://embossgui.sourceforge.net/
-
-Package: emboss-explorer
-Architecture: all
-Depends: ${perl:Depends}, libmailtools-perl, libemboss-acd-perl, emboss (>= 5.0.0),
- emboss-data, apache2 | httpd-cgi
-Recommends: emboss-doc
-Description: web-based GUI to EMBOSS
- EMBOSS explorer is a web-based graphical user interface
- to the EMBOSS suite of bioinformatics tools. It is written
- in Perl.
- .
- If you use the Apache HTTP server, you will at most have to restart it before
- using EMBOSS explorer. For other web servers, you will have to do the
- configuration by yourself.
-
-Package: libemboss-acd-perl
-Architecture: all
-Section: perl
-Depends: ${perl:Depends}, libparse-recdescent-perl
-Description: perl module to parse EMBOSS ACD files
- EMBOSS::ACD parses EMBOSS Ajax Command Definition files
- and provides object-oriented access to the data contained
- therein.
- .
- For a complete specification of the ACD format, see
- http://emboss.sourceforge.net/developers/acd
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/control (from rev 14711, trunk/packages/emboss-explorer/trunk/debian/control)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/control (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/control 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,44 @@
+Source: emboss-explorer
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <plessy at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9), apache2-dev
+Build-Depends-Indep: libparse-recdescent-perl,
+ libmailtools-perl
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/emboss-explorer/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/emboss-explorer/trunk/
+Homepage: http://embossgui.sourceforge.net/
+
+Package: emboss-explorer
+Architecture: all
+Depends: ${perl:Depends},
+ libmailtools-perl,
+ libemboss-acd-perl,
+ emboss,
+ emboss-data,
+ ${misc:Depends}
+Recommends: emboss-doc, ${misc:Recommends}
+Description: web-based GUI to EMBOSS
+ EMBOSS explorer is a web-based graphical user interface
+ to the EMBOSS suite of bioinformatics tools. It is written
+ in Perl.
+ .
+ If you use the Apache HTTP server, you will at most have to restart it before
+ using EMBOSS explorer. For other web servers, you will have to do the
+ configuration by yourself.
+
+Package: libemboss-acd-perl
+Architecture: all
+Section: perl
+Depends: ${perl:Depends},
+ libparse-recdescent-perl,
+ ${misc:Depends}
+Description: perl module to parse EMBOSS ACD files
+ EMBOSS::ACD parses EMBOSS Ajax Command Definition files
+ and provides object-oriented access to the data contained
+ therein.
+ .
+ For a complete specification of the ACD format, see
+ http://emboss.sourceforge.net/developers/acd
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.apache2 (from rev 14705, trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.apache2)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.apache2 (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.apache2 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1 @@
+conf debian/emboss-explorer.apache2.conf
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.apache2.conf (from rev 14710, trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.apache2.conf)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.apache2.conf (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.apache2.conf 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,21 @@
+# I used /etc/gallery2/apache.conf as a template. -- Charles Plessy
+Alias /emboss-explorer /usr/share/emboss-explorer/html
+
+<Directory /usr/share/emboss-explorer/html>
+ Options FollowSymLinks
+# AllowOverride Limit Options FileInfo
+</Directory>
+
+Alias /doc/emboss-explorer "/usr/share/EMBOSS/doc/programs"
+<Directory "/usr/share/doc/emboss-explorer/">
+ Options Indexes MultiViews FollowSymLinks
+ AllowOverride None
+ Require all granted
+</Directory>
+
+# some people prefer a simple URL like http://emboss-explorer.example
+#<VirtualHost 1.2.3.4>
+# DocumentRoot /usr/share/emboss-explorer
+# ServerName emboss-explorer.example
+#</VirtualHost>
+
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.desktop
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.desktop 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.desktop 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,17 +0,0 @@
-# This file was orignially written for Debian, and can be copied, used,
-# modified and redistributed under the same licence as EMBOSS Explorer itself.
-
-[Desktop Entry]
-Version=1.0
-Terminal=false
-Icon=emboss-explorer
-Exec=sensible-browser http://localhost/emboss-explorer
-Name=EMBOSS Explorer
-GenericName=EMBOSS frontend
-GenericName[en]=EMBOSS frontend
-GenericName[fr]=Interface graphique pour EMBOSS
-Comment=Starts the default web browser on the local EMBOSS Explorer website.
-Comment[en]=Starts the default web browser on the local EMBOSS Explorer website.
-Comment[fr]=Lance le navigateur par défaut sur le site local EMBOSS Explorer.
-Type=Application
-Categories=Biology;Science;Education;
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.desktop (from rev 14698, trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.desktop)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.desktop (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.desktop 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,18 @@
+# This file was orignially written for Debian, and can be copied, used,
+# modified and redistributed under the same licence as EMBOSS Explorer itself.
+
+[Desktop Entry]
+Version=1.0
+Terminal=false
+Icon=emboss-explorer
+Exec=sensible-browser http://localhost/emboss-explorer
+Name=EMBOSS Explorer
+GenericName=EMBOSS frontend
+GenericName[en]=EMBOSS frontend
+GenericName[fr]=Interface graphique pour EMBOSS
+Keywords=GUI;web;
+Comment=Starts the default web browser on the local EMBOSS Explorer website.
+Comment[en]=Starts the default web browser on the local EMBOSS Explorer website.
+Comment[fr]=Lance le navigateur par défaut sur le site local EMBOSS Explorer.
+Type=Application
+Categories=Biology;Science;Education;
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.install
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.install 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.install 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,7 +0,0 @@
-/cgi/emboss usr/lib/cgi-bin/
-html/style/* etc/emboss-explorer/style/
-debian/emboss-explorer.conf etc/emboss-explorer/
-debian/apache.conf etc/emboss-explorer/
-debian/index.html usr/share/emboss-explorer/html
-html/images/* usr/share/emboss-explorer/images
-debian/emboss-explorer.desktop usr/share/applications
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.install (from rev 14705, trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.install)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.install (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.install 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,6 @@
+/cgi/emboss usr/lib/cgi-bin/
+html/style/* etc/emboss-explorer/style/
+debian/emboss-explorer.conf etc/emboss-explorer/
+debian/index.html usr/share/emboss-explorer/html
+html/images/* usr/share/emboss-explorer/images
+debian/emboss-explorer.desktop usr/share/applications
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.links
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.links 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.links 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,4 +0,0 @@
-usr/share/EMBOSS/doc/html/emboss/apps/ usr/share/doc/emboss-explorer/html
-etc/emboss-explorer/apache.conf etc/apache2/conf.d/emboss-explorer
-etc/emboss-explorer/style/ usr/share/emboss-explorer/html/style
-var/lib/emboss-explorer/output usr/share/emboss-explorer/html/output
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.links (from rev 14704, trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.links)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.links (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.links 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,4 @@
+usr/share/EMBOSS/doc/html/emboss/apps/ usr/share/doc/emboss-explorer/html
+etc/apache2/conf-available/emboss-explorer.apache2.conf etc/emboss-explorer/apache2.conf
+etc/emboss-explorer/style/ usr/share/emboss-explorer/html/style
+var/lib/emboss-explorer/output usr/share/emboss-explorer/html/output
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.lintian-overrides (from rev 14695, trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.lintian-overrides)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.lintian-overrides (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.lintian-overrides 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,2 @@
+# We already have another file called emboss-explorer.conf.
+emboss-explorer: non-standard-apache2-configuration-name emboss-explorer.apache2.conf != emboss-explorer.conf
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.postinst
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.postinst 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.postinst 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,50 +0,0 @@
-#!/bin/sh
-# postinst script for emboss-explorer
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-# * <postinst> `configure' <most-recently-configured-version>
-# * <old-postinst> `abort-upgrade' <new version>
-# * <conflictor's-postinst> `abort-remove' `in-favour' <package>
-# <new-version>
-# * <postinst> `abort-remove'
-# * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
-# <failed-install-package> <version> `removing'
-# <conflicting-package> <version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
- configure)
- if [ -x /etc/init.d/apache2 ]
- then
- if which /usr/sbin/invoke-rc.d >/dev/null 2>&1
- then
- invoke-rc.d apache2 reload || true
- else
- /etc/init.d/apache2 reload || true
- fi
- fi
- ;;
-
- abort-upgrade|abort-remove|abort-deconfigure)
- ;;
-
- *)
- echo "postinst called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
-
-
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.postrm
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/emboss-explorer.postrm 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/emboss-explorer.postrm 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,43 +0,0 @@
-#!/bin/sh
-# postrm script for emboss-explorer
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-# * <postrm> `remove'
-# * <postrm> `purge'
-# * <old-postrm> `upgrade' <new-version>
-# * <new-postrm> `failed-upgrade' <old-version>
-# * <new-postrm> `abort-install'
-# * <new-postrm> `abort-install' <old-version>
-# * <new-postrm> `abort-upgrade' <old-version>
-# * <disappearer's-postrm> `disappear' <overwriter>
-# <overwriter-version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
- purge)
- [ -d "/var/lib/emboss-explorer/output" ] && find /var/lib/emboss-explorer/output -mindepth 1 -maxdepth 1 -exec rm -rf {} \;
- ;;
-
- purge|remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
- ;;
-
- *)
- echo "postrm called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
-
-
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/index.html
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/index.html 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/index.html 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,11 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">
-<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>
- <head>
- <title>EMBOSS Explorer</title>
- </head>
- <frameset cols="170, *">
- <frame src="/cgi-bin/emboss/menu" name="menu" />
- <frame src="/cgi-bin/emboss/intro" name="main" />
- </frameset>
-</html>
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/index.html (from rev 14712, trunk/packages/emboss-explorer/trunk/debian/index.html)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/index.html (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/index.html 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,11 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">
+<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>
+ <head>
+ <title>EMBOSS Explorer</title>
+ </head>
+ <frameset cols="170, *">
+ <frame src="/cgi-bin/emboss/menu" name="menu" />
+ <frame src="/cgi-bin/emboss/intro" name="main" />
+ </frameset>
+</html>
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/01-fix_examples.diff
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/01-fix_examples.diff 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/01-fix_examples.diff 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,19 +0,0 @@
-Author: David Paleino <d.paleino at gmail.com>
-Description:
- The Debian package for EMBOSS installs its files in /usr/share/EMBOSS.
- This patch is necessary for the test of the ACD module to function.
-Forwarded: no
- As it is Debian-specific, it has not been forwarded upstream.
-
-diff -urNad emboss-explorer~/t/ACD.t emboss-explorer/t/ACD.t
---- emboss-explorer~/t/ACD.t 2006-11-13 00:38:39.000000000 +0100
-+++ emboss-explorer/t/ACD.t 2007-05-20 15:33:09.000000000 +0200
-@@ -15,7 +15,7 @@
- BEGIN {
- # locate the EMBOSS ACD files in order to validate against them...
- #
-- @ACDFILES = glob "/usr/local/share/EMBOSS/acd/*.acd";
-+ @ACDFILES = glob "/usr/share/EMBOSS/acd/*.acd";
-
- $XHTML = EMBOSS::GUI::XHTML->new(
- script_url => 'dummy'
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/01-fix_examples.diff (from rev 14707, trunk/packages/emboss-explorer/trunk/debian/patches/01-fix_examples.diff)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/01-fix_examples.diff (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/01-fix_examples.diff 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,19 @@
+Author: David Paleino <d.paleino at gmail.com>
+Description:
+ The Debian package for EMBOSS installs its files in /usr/share/EMBOSS.
+ This patch is necessary for the test of the ACD module to function.
+Forwarded: no
+ As it is Debian-specific, it has not been forwarded upstream.
+
+diff -urNad emboss-explorer~/t/ACD.t emboss-explorer/t/ACD.t
+--- emboss-explorer~/t/ACD.t 2006-11-13 00:38:39.000000000 +0100
++++ emboss-explorer/t/ACD.t 2007-05-20 15:33:09.000000000 +0200
+@@ -15,7 +15,7 @@
+ BEGIN {
+ # locate the EMBOSS ACD files in order to validate against them...
+ #
+- @ACDFILES = glob "/usr/local/share/EMBOSS/acd/*.acd";
++ @ACDFILES = glob "/usr/share/EMBOSS/acd/*.acd";
+
+ $XHTML = EMBOSS::GUI::XHTML->new(
+ script_url => 'dummy'
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/02-fix_Conf.pm.diff
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.diff 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/02-fix_Conf.pm.diff 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,91 +0,0 @@
-Author: David Paleino <d.paleino at gmail.com>
-Description: Moving configuration to /etc/emboss-explorer.conf
-Forwarded: http://sourceforge.net/tracker/index.php?func=detail&aid=1992075&group_id=124389&atid=699414
-
-diff -urNad emboss-explorer~/lib/EMBOSS/GUI/Conf.pm emboss-explorer/lib/EMBOSS/GUI/Conf.pm
---- emboss-explorer~/lib/EMBOSS/GUI/Conf.pm 2007-05-25 09:13:23.000000000 +0200
-+++ emboss-explorer/lib/EMBOSS/GUI/Conf.pm 2007-05-25 09:13:57.000000000 +0200
-@@ -43,79 +43,16 @@
-
- package EMBOSS::GUI::Conf;
-
--use strict;
- use warnings;
-
- use Carp;
-
- our $VERSION = 1.10;
-
--# path to the EMBOSS::GUI HTML files
--our $HTML_PATH = "/var/www/emboss/html";
--
--# URL corresponding to $HTML_PATH above
--our $HTML_URL = "/emboss";
--
--# URL specifying the style sheet to use
--our $STYLE_URL = "$HTML_URL/style/emboss.css";
--
--# URL prefix to place before image links
--our $IMAGE_URL = "$HTML_URL/images";
--
--# URL prefix to place before manual links (only used in static pages)
--our $MANUAL_URL = "$HTML_URL/manual";
--
--# path to the EMBOSS::GUI temporary output directory
--our $OUTPUT_PATH = "$HTML_PATH/output";
--
--# URL corresponding to $OUTPUT_PATH above
--our $OUTPUT_URL = "$HTML_URL/output";
--
--# prefix under which EMBOSS was installed
--our $EMBOSS_PREFIX = "/usr/local";
--
--# path to EMBOSS binaries
--our $EMBOSS_BIN = "$EMBOSS_PREFIX/bin";
--
--# path to EMBOSS installation
--our $EMBOSS_HOME = "$EMBOSS_PREFIX/share/EMBOSS";
--
--# path to EMBOSS ACD files
--our $EMBOSS_ACDROOT = "$EMBOSS_HOME/acd";
--
--# path to EMBOSS data
--our $EMBOSS_DATA = "$EMBOSS_HOME/data";
--
--# path to EMBOSS application manuals
--our $EMBOSS_MANUAL = "$EMBOSS_HOME/doc/html";
--
--# list of groups and applications to exclude from the main menu
--our @EXCLUDED = (
-- "ACD",
-- "acdc",
-- "acdpretty",
-- "acdtable",
-- "acdtrace",
-- "acdvalid",
-- "UTILS DATABASE CREATION",
-- "aaindexextract",
-- "cutgextract",
-- "printsextract",
-- "prosextract",
-- "rebaseextract",
-- "tfextract",
-- "UTILS DATABASE INDEXING",
-- "dbiblast",
-- "dbifasta",
-- "dbiflat",
-- "dbigcg",
--);
--
--# number of seconds to delay between placeholder page refreshes
--our $REFRESH_DELAY = 1;
--
--# whether or not to display using frames
--our $FRAMES = 1;
-+open (config_file, "</etc/emboss-explorer/emboss-explorer.conf") or die "Cannot load /etc/emboss-explorer.conf!";
-+my @conf = <config_file>;
-+eval join("\n", @conf);
-+die $@ if $@;
-
- =item new()
-
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/02-fix_Conf.pm.diff (from rev 14707, trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.diff)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/02-fix_Conf.pm.diff (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/02-fix_Conf.pm.diff 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,91 @@
+Author: David Paleino <d.paleino at gmail.com>
+Description: Moving configuration to /etc/emboss-explorer.conf
+Forwarded: http://sourceforge.net/tracker/index.php?func=detail&aid=1992075&group_id=124389&atid=699414
+
+diff -urNad emboss-explorer~/lib/EMBOSS/GUI/Conf.pm emboss-explorer/lib/EMBOSS/GUI/Conf.pm
+--- emboss-explorer~/lib/EMBOSS/GUI/Conf.pm 2007-05-25 09:13:23.000000000 +0200
++++ emboss-explorer/lib/EMBOSS/GUI/Conf.pm 2007-05-25 09:13:57.000000000 +0200
+@@ -43,79 +43,16 @@
+
+ package EMBOSS::GUI::Conf;
+
+-use strict;
+ use warnings;
+
+ use Carp;
+
+ our $VERSION = 1.10;
+
+-# path to the EMBOSS::GUI HTML files
+-our $HTML_PATH = "/var/www/emboss/html";
+-
+-# URL corresponding to $HTML_PATH above
+-our $HTML_URL = "/emboss";
+-
+-# URL specifying the style sheet to use
+-our $STYLE_URL = "$HTML_URL/style/emboss.css";
+-
+-# URL prefix to place before image links
+-our $IMAGE_URL = "$HTML_URL/images";
+-
+-# URL prefix to place before manual links (only used in static pages)
+-our $MANUAL_URL = "$HTML_URL/manual";
+-
+-# path to the EMBOSS::GUI temporary output directory
+-our $OUTPUT_PATH = "$HTML_PATH/output";
+-
+-# URL corresponding to $OUTPUT_PATH above
+-our $OUTPUT_URL = "$HTML_URL/output";
+-
+-# prefix under which EMBOSS was installed
+-our $EMBOSS_PREFIX = "/usr/local";
+-
+-# path to EMBOSS binaries
+-our $EMBOSS_BIN = "$EMBOSS_PREFIX/bin";
+-
+-# path to EMBOSS installation
+-our $EMBOSS_HOME = "$EMBOSS_PREFIX/share/EMBOSS";
+-
+-# path to EMBOSS ACD files
+-our $EMBOSS_ACDROOT = "$EMBOSS_HOME/acd";
+-
+-# path to EMBOSS data
+-our $EMBOSS_DATA = "$EMBOSS_HOME/data";
+-
+-# path to EMBOSS application manuals
+-our $EMBOSS_MANUAL = "$EMBOSS_HOME/doc/html";
+-
+-# list of groups and applications to exclude from the main menu
+-our @EXCLUDED = (
+- "ACD",
+- "acdc",
+- "acdpretty",
+- "acdtable",
+- "acdtrace",
+- "acdvalid",
+- "UTILS DATABASE CREATION",
+- "aaindexextract",
+- "cutgextract",
+- "printsextract",
+- "prosextract",
+- "rebaseextract",
+- "tfextract",
+- "UTILS DATABASE INDEXING",
+- "dbiblast",
+- "dbifasta",
+- "dbiflat",
+- "dbigcg",
+-);
+-
+-# number of seconds to delay between placeholder page refreshes
+-our $REFRESH_DELAY = 1;
+-
+-# whether or not to display using frames
+-our $FRAMES = 1;
++open (config_file, "</etc/emboss-explorer/emboss-explorer.conf") or die "Cannot load /etc/emboss-explorer.conf!";
++my @conf = <config_file>;
++eval join("\n", @conf);
++die $@ if $@;
+
+ =item new()
+
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/05-build-manpages.diff
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/05-build-manpages.diff 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/05-build-manpages.diff 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,15 +0,0 @@
-Author: Charles Plessy <plessy at debian.org>
-Description: Automatically build and install the POD manpages of acdcheckd and mkstatic.
-Forwarded: http://sourceforge.net/tracker/index.php?func=detail&aid=1994395&group_id=124389&atid=699414
-
-diff -urNad emboss-explorer~/t/ACD.t emboss-explorer/t/ACD.t
---- emboss-explorer-2.2.0/Makefile.PL.old 2008-06-16 07:53:53.000000000 +0900
-+++ emboss-explorer-2.2.0/Makefile.PL 2008-06-16 07:55:33.000000000 +0900
-@@ -10,5 +10,6 @@
- },
- PREREQ_FATAL => 1,
- ABSTRACT_FROM => 'lib/EMBOSS/GUI.pm',
-- AUTHOR => 'Luke McCarthy <lukem at gene.pbi.nrc.ca>'
-+ AUTHOR => 'Luke McCarthy <lukem at gene.pbi.nrc.ca>',
-+ EXE_FILES => => [ qw( bin/acdcheck bin/mkstatic ) ]
- );
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/05-build-manpages.diff (from rev 14707, trunk/packages/emboss-explorer/trunk/debian/patches/05-build-manpages.diff)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/05-build-manpages.diff (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/05-build-manpages.diff 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,15 @@
+Author: Charles Plessy <plessy at debian.org>
+Description: Automatically build and install the POD manpages of acdcheckd and mkstatic.
+Forwarded: http://sourceforge.net/tracker/index.php?func=detail&aid=1994395&group_id=124389&atid=699414
+
+diff -urNad emboss-explorer~/t/ACD.t emboss-explorer/t/ACD.t
+--- emboss-explorer-2.2.0/Makefile.PL.old 2008-06-16 07:53:53.000000000 +0900
++++ emboss-explorer-2.2.0/Makefile.PL 2008-06-16 07:55:33.000000000 +0900
+@@ -10,5 +10,6 @@
+ },
+ PREREQ_FATAL => 1,
+ ABSTRACT_FROM => 'lib/EMBOSS/GUI.pm',
+- AUTHOR => 'Luke McCarthy <lukem at gene.pbi.nrc.ca>'
++ AUTHOR => 'Luke McCarthy <lukem at gene.pbi.nrc.ca>',
++ EXE_FILES => => [ qw( bin/acdcheck bin/mkstatic ) ]
+ );
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/emboss-6.4-group-list.patch (from rev 14708, trunk/packages/emboss-explorer/trunk/debian/patches/emboss-6.4-group-list.patch)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/emboss-6.4-group-list.patch (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/emboss-6.4-group-list.patch 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,15 @@
+Description: correct menu when using EMBOSS >= 6.4.
+Origin: http://sourceforge.net/p/embossgui/bugs/_discuss/thread/b0c058e8/fc9b/attachment/emboss-6.4-group-list.patch
+Bug: http://sourceforge.net/p/embossgui/bugs/21/
+Bug-Debian: http://bugs.debian.org/722982
+--- emboss-explorer/lib/EMBOSS/GUI/XHTML.pm.orig 2012-11-15 09:35:20.390050595 -0700
++++ emboss-explorer/lib/EMBOSS/GUI/XHTML.pm 2012-11-15 09:35:58.083051229 -0700
+@@ -314,7 +314,7 @@
+ my $html = <<EOF;
+ <div id='menu'>
+ EOF
+- if (@{$entries[0]} > 2) { # entries are groups...
++ if (ref($entries[0][1]) eq "ARRAY") { # entries are groups...
+ my $menu_url = $self->{static} ?
+ "alphamenu.html" : "$self->{script_url}/menu?sort=alpha";
+ $html .= <<EOF;
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/series
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/series 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/series 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,3 +0,0 @@
-01-fix_examples.diff
-02-fix_Conf.pm.diff
-05-build-manpages.diff
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/series (from rev 14708, trunk/packages/emboss-explorer/trunk/debian/patches/series)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/series (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/patches/series 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,4 @@
+01-fix_examples.diff
+02-fix_Conf.pm.diff
+05-build-manpages.diff
+emboss-6.4-group-list.patch
Deleted: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/rules
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/rules 2013-09-12 17:55:17 UTC (rev 14679)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/rules 2013-09-15 05:08:14 UTC (rev 14715)
@@ -1,24 +0,0 @@
-#!/usr/bin/make -f
-
-PERL ?= /usr/bin/perl
-PACKAGE = emboss-explorer
-TMP = $(CURDIR)/debian/$(PACKAGE)
-
-%:
- dh $@
-
-override_dh_auto_test:
-# disabled because of http://sourceforge.net/tracker/index.php?func=detail&aid=1994385&group_id=124389&atid=699414
-
-override_dh_install:
- dh_install
- $(MAKE) install DESTDIR=$(TMP) PREFIX=/usr
- # Move ACD.pm to a separate package, that is useful for making
- # manpages from EMBOSS ACD files without being bothered by the
- # dependancy on web servers.
- mv $(CURDIR)/debian/tmp/usr/share/perl5/EMBOSS/ACD.pm $(CURDIR)/debian/libemboss-acd-perl/usr/share/perl5/EMBOSS/
- mv $(CURDIR)/debian/tmp/usr/share/man/man3/EMBOSS::ACD.3pm $(CURDIR)/debian/libemboss-acd-perl/usr/share/man/man3/
-
-override_dh_fixperms:
- dh_fixperms
- install -m 755 -o www-data -g www-data -d $(CURDIR)/debian/emboss-explorer/var/lib/emboss-explorer/output
Copied: trunk/packages/emboss-explorer/tags/2.2.0-8/debian/rules (from rev 14713, trunk/packages/emboss-explorer/trunk/debian/rules)
===================================================================
--- trunk/packages/emboss-explorer/tags/2.2.0-8/debian/rules (rev 0)
+++ trunk/packages/emboss-explorer/tags/2.2.0-8/debian/rules 2013-09-15 05:08:14 UTC (rev 14715)
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+export DH_VERBOSE=1
+
+%:
+ dh $@ --with apache2
+
+override_dh_auto_test:
+# disabled because of http://sourceforge.net/tracker/index.php?func=detail&aid=1994385&group_id=124389&atid=699414
+
+override_dh_install:
+ dh_install
+ $(MAKE) install DESTDIR=$(CURDIR)/debian/emboss-explorer PREFIX=/usr
+ # Move ACD.pm to a separate package, that is useful for making
+ # manpages from EMBOSS ACD files without being bothered by the
+ # dependancy on web servers.
+ mv $(CURDIR)/debian/emboss-explorer/usr/share/perl5/EMBOSS/ACD.pm $(CURDIR)/debian/libemboss-acd-perl/usr/share/perl5/EMBOSS/
+ mv $(CURDIR)/debian/emboss-explorer/usr/share/man/man3/EMBOSS::ACD.3pm $(CURDIR)/debian/libemboss-acd-perl/usr/share/man/man3/
+
+override_dh_fixperms:
+ dh_fixperms
+ install -m 755 -o www-data -g www-data -d $(CURDIR)/debian/emboss-explorer/var/lib/emboss-explorer/output
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