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 <[email protected]> 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 <[email protected]> Uploaders: Olivier Sallou <[email protected]>, Charles Plessy <[email protected]>, Aaron M. Ucko <[email protected]> -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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
