[med-svn] r13778 - trunk/packages/gmod/gbrowse/trunk/debian
olivier sallou
osallou-guest at alioth.debian.org
Fri May 31 12:23:32 UTC 2013
Author: osallou-guest
Date: 2013-05-31 12:23:32 +0000 (Fri, 31 May 2013)
New Revision: 13778
Added:
trunk/packages/gmod/gbrowse/trunk/debian/gbrowse.apache2
trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_apache2.conf
Modified:
trunk/packages/gmod/gbrowse/trunk/debian/changelog
trunk/packages/gmod/gbrowse/trunk/debian/control
trunk/packages/gmod/gbrowse/trunk/debian/gbrowse.links
trunk/packages/gmod/gbrowse/trunk/debian/lintian-overrides
trunk/packages/gmod/gbrowse/trunk/debian/rules
Log:
apache 2.4 transition
Modified: trunk/packages/gmod/gbrowse/trunk/debian/changelog
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/changelog 2013-05-31 12:05:12 UTC (rev 13777)
+++ trunk/packages/gmod/gbrowse/trunk/debian/changelog 2013-05-31 12:23:32 UTC (rev 13778)
@@ -1,3 +1,9 @@
+gbrowse (2.54+dfsg-2) unstable; urgency=low
+
+ * Transition to apache 2.4 (Closes: #669830).
+
+ -- Olivier Sallou <osallou at debian.org> Sat, 25 May 2013 11:46:26 +0200
+
gbrowse (2.54+dfsg-1) unstable; urgency=low
* New upstream release
Modified: trunk/packages/gmod/gbrowse/trunk/debian/control
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/control 2013-05-31 12:05:12 UTC (rev 13777)
+++ trunk/packages/gmod/gbrowse/trunk/debian/control 2013-05-31 12:23:32 UTC (rev 13778)
@@ -1,16 +1,24 @@
Source: gbrowse
Section: science
Priority: optional
-Build-Depends: bioperl (>= 1.6.901), debhelper (>= 8),
- libbio-graphics-perl (>= 2.31), libcapture-tiny-perl, libcgi-session-perl (>= 4.02),
- libgd-gd2-perl (>= 2.07) | libgd-gd2-noxpm-perl (>= 2.07), libio-string-perl,
- libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl,
- perl (>= 5.10.0) | libextutils-cbuilder-perl, sqlite3,libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype (>=1.7), libjs-scriptaculous (>= 1.9),
+Build-Depends: bioperl (>= 1.6.901), debhelper (>= 9), dh-apache2,
+ libbio-graphics-perl (>= 2.31),
+ libcapture-tiny-perl,
+ libcgi-session-perl (>= 4.02),
+ libgd-gd2-perl (>= 2.07) | libgd-gd2-noxpm-perl (>= 2.07),
+ libio-string-perl,
+ libjson-perl,
+ libstatistics-descriptive-perl,
+ libwww-perl,
+ libhttp-daemon-perl, perl,
+ perl (>= 5.10.0) | libextutils-cbuilder-perl,
+ sqlite3, libdbd-sqlite3-perl,
+ libterm-readkey-perl,
+ libjs-prototype (>=1.7), libjs-scriptaculous (>= 1.9),
libvm-ec2-perl
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Olivier Sallou <osallou at debian.org>,
Charles Plessy <plessy at debian.org>, Aaron M. Ucko <ucko at debian.org>
-DM-Upload-Allowed: yes
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/gmod/gbrowse/trunk/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gmod/gbrowse/
Standards-Version: 3.9.3
@@ -19,12 +27,21 @@
Package: gbrowse
Architecture: all
Depends: ${misc:Depends}, ${perl:Depends},
+ apache2 (>= 2.4) | httpd-cgi,
bioperl (>= 1.6.901), libbio-graphics-perl (>= 2.31),
libcgi-session-perl (>= 4.02),
- libgd-gd2-noxpm-perl (>= 2.07) | libgd-gd2-perl (>= 2.07), libio-string-perl,
- libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl,
- perl (>= 5.10.0) | libextutils-cbuilder-perl, libterm-readkey-perl, sqlite3, libdbd-sqlite3-perl, libjs-prototype (>=1.7), libjs-scriptaculous (>=1.9),
+ libgd-gd2-noxpm-perl (>= 2.07) | libgd-gd2-perl (>= 2.07),
+ libio-string-perl,
+ libjson-perl,
+ libstatistics-descriptive-perl,
+ libwww-perl,
+ libhttp-daemon-perl,
+ perl (>= 5.10.0) | libextutils-cbuilder-perl,
+ libterm-readkey-perl,
+ sqlite3, libdbd-sqlite3-perl,
+ libjs-prototype (>=1.7), libjs-scriptaculous (>=1.9),
libvm-ec2-perl
+Recommends: ${misc:Recommends}
Suggests: gbrowse-data, gbrowse-calign, libfile-nfslock-perl
Description: GMOD Generic Genome Browser
Generic Genome Browser is a simple but highly
Added: trunk/packages/gmod/gbrowse/trunk/debian/gbrowse.apache2
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/gbrowse.apache2 (rev 0)
+++ trunk/packages/gmod/gbrowse/trunk/debian/gbrowse.apache2 2013-05-31 12:23:32 UTC (rev 13778)
@@ -0,0 +1 @@
+conf debian/gbrowse_apache2.conf
Modified: trunk/packages/gmod/gbrowse/trunk/debian/gbrowse.links
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/gbrowse.links 2013-05-31 12:05:12 UTC (rev 13777)
+++ trunk/packages/gmod/gbrowse/trunk/debian/gbrowse.links 2013-05-31 12:23:32 UTC (rev 13778)
@@ -1,3 +1,2 @@
-etc/gbrowse/apache2.conf etc/apache2/conf.d/gbrowse
usr/share/javascript/prototype/prototype.js usr/share/gbrowse/htdocs/js/prototype.js
usr/share/javascript/scriptaculous/scriptaculous.js usr/share/gbrowse/htdocs/js/scriptaculous.js
Added: trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_apache2.conf
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_apache2.conf (rev 0)
+++ trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_apache2.conf 2013-05-31 12:23:32 UTC (rev 13778)
@@ -0,0 +1,62 @@
+Alias "/gbrowse2/i/" "/var/cache/gbrowse/images/"
+Alias "/gbrowse2" "/usr/share/gbrowse/htdocs"
+ScriptAlias "/gb2" "/usr/lib/cgi-bin/gbrowse"
+
+<Directory "/usr/share/gbrowse/htdocs">
+ AllowOverride Options
+ Options -Indexes -MultiViews +FollowSymLinks
+ Require all granted
+</Directory>
+
+<Directory "/usr/share/gbrowse/htdocs/tutorial">
+ Options +Indexes
+</Directory>
+
+<Directory "/var/cache/gbrowse/images/">
+ Require all granted
+</Directory>
+
+<Directory "/var/lib/gbrowse/databases">
+ Require all granted
+</Directory>
+
+<Directory "/usr/lib/cgi-bin/gbrowse">
+
+ Options ExecCGI
+ SetEnv GBROWSE_CONF "/etc/gbrowse"
+</Directory>
+
+<IfModule mod_fcgid.c>
+ Alias /fgb2 "/usr/lib/cgi-bin/gbrowse"
+ <Location /fgb2>
+ SetHandler fcgid-script
+ </Location>
+ FcgidInitialEnv GBROWSE_CONF /etc/gbrowse
+ # these directives prevent idle/busy timeouts and may need to be
+ # adjusted up or down
+ FcgidMinProcessesPerClass 6
+ FcgidIOTimeout 600
+ FcgidBusyTimeout 600
+
+</IfModule>
+
+<IfModule mod_fastcgi.c>
+ Alias /fgb2 "/usr/lib/cgi-bin/gbrowse"
+ <Location /fgb2>
+ SetHandler fastcgi-script
+ </Location>
+ # Note: you may need to increase -idle-timeout if file uploads are timing out and returning server
+ # errors.
+ FastCgiConfig -idle-timeout 600 -maxClassProcesses 20 -initial-env GBROWSE_CONF=/etc/gbrowse
+</IfModule>
+
+# Use of mod_perl is no longer supported. Use at your own risk.
+<IfModule mod_perl.c>
+ Alias /mgb2 "/usr/lib/cgi-bin/gbrowse"
+
+ <Location /mgb2>
+ SetHandler perl-script
+ PerlResponseHandler ModPerl::Registry
+ PerlOptions +ParseHeaders
+ </Location>
+</IfModule>
Modified: trunk/packages/gmod/gbrowse/trunk/debian/lintian-overrides
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/lintian-overrides 2013-05-31 12:05:12 UTC (rev 13777)
+++ trunk/packages/gmod/gbrowse/trunk/debian/lintian-overrides 2013-05-31 12:23:32 UTC (rev 13778)
@@ -1,2 +1 @@
-gbrowse: manpage-has-errors-from-man usr/share/man/man3/Bio::Graphics::Browser2::PluginSet.3pm.gz 139: warning [p 1, 1.8i, div `an-div', 0.2i]: can't break line
gbrowse: script-not-executable etc/gbrowse/MobyServices/GbrowseServices.pm
Modified: trunk/packages/gmod/gbrowse/trunk/debian/rules
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/rules 2013-05-31 12:05:12 UTC (rev 13777)
+++ trunk/packages/gmod/gbrowse/trunk/debian/rules 2013-05-31 12:23:32 UTC (rev 13778)
@@ -3,14 +3,14 @@
GBROWSE_BUILD_OPTIONS = --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse
%:
- dh $@
+ dh $@ --with apache2
override_dh_auto_configure:
dh_auto_configure -- $(GBROWSE_BUILD_OPTIONS)
override_dh_auto_install:
./Build --install_base=debian/gbrowse debianinstall
- ./Build apache_conf > debian/gbrowse/etc/gbrowse/apache2.conf
+ #./Build apache_conf > debian/gbrowse/etc/gbrowse/gbrowse_apache2.conf
perl Build.PL $(GBROWSE_BUILD_OPTIONS) --installetc=y
./Build --install_base=debian/gbrowse install_slave
mv debian/gbrowse/lib/perl5/* debian/gbrowse/usr/share/perl5
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