Author: osallou-guest Date: 2011-08-10 07:01:49 +0000 (Wed, 10 Aug 2011) New Revision: 7401
Added: trunk/packages/mobyle/mobyle/trunk/debian/ trunk/packages/mobyle/mobyle/trunk/debian/changelog trunk/packages/mobyle/mobyle/trunk/debian/compat trunk/packages/mobyle/mobyle/trunk/debian/control trunk/packages/mobyle/mobyle/trunk/debian/copyright trunk/packages/mobyle/mobyle/trunk/debian/docs trunk/packages/mobyle/mobyle/trunk/debian/get-orig-source trunk/packages/mobyle/mobyle/trunk/debian/mobyle-utils.dirs trunk/packages/mobyle/mobyle/trunk/debian/mobyle-utils.links trunk/packages/mobyle/mobyle/trunk/debian/mobyle.apache2 trunk/packages/mobyle/mobyle/trunk/debian/mobyle.dirs trunk/packages/mobyle/mobyle/trunk/debian/mobyle.links trunk/packages/mobyle/mobyle/trunk/debian/patches/ trunk/packages/mobyle/mobyle/trunk/debian/patches/change_mobylehome trunk/packages/mobyle/mobyle/trunk/debian/patches/defaultconfig trunk/packages/mobyle/mobyle/trunk/debian/patches/series trunk/packages/mobyle/mobyle/trunk/debian/postinst trunk/packages/mobyle/mobyle/trunk/debian/rules trunk/packages/mobyle/mobyle/trunk/debian/source/ trunk/packages/mobyle/mobyle/trunk/debian/source/format trunk/packages/mobyle/mobyle/trunk/debian/watch Log: [svn-inject] Applying Debian modifications (1.0.0-1) to trunk Property changes on: trunk/packages/mobyle/mobyle/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/mobyle/mobyle/trunk/debian/changelog =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/changelog (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/changelog 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,5 @@ +mobyle (1.0.0-1) unstable; urgency=low + + * Initial release (Closes: #637230) + + -- Olivier Sallou <[email protected]> Mon, 08 Aug 2011 14:55:59 +0200 Added: trunk/packages/mobyle/mobyle/trunk/debian/compat =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/compat (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/compat 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1 @@ +8 Added: trunk/packages/mobyle/mobyle/trunk/debian/control =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/control (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/control 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,28 @@ +Source: mobyle +Section: science +Priority: optional +Maintainer: Olivier Sallou <[email protected]> +Build-Depends: debhelper (>= 8.0.0),python-all, simpletal (>=4.1), simplejson (>= 1.7.1), python-imaging (>= 1.1.5), python-lxml (>= 2.2.4), python-pycaptcha, libjs-scriptaculous, libjs-jquery, libjs-prototype +Standards-Version: 3.9.2 +Homepage: https://projets.pasteur.fr/projects/show/mobyle +#Vcs-Git: git://git.debian.org/collab-maint/mobyle.git +#Vcs-Browser: http://git.debian.org/?p=collab-maint/mobyle.git;a=summary + +Package: mobyle +Architecture: all +Depends: ${misc:Depends}, python (>= 2.5), apache2, python-simpletal (>=4.1), python-simplejson (>= 1.7.1), python-imaging (>= 1.1.5), + python-lxml (>= 2.2.4), squizz, python-pycaptcha, libjs-scriptaculous, libjs-jquery, libjs-prototype, mobyle-utils +Suggests: python-openid (>= 2.2.4), python-dnspython (>= 1.5.0) +Recommends: mobyle-programs (>= 1.0), jing, mobyle-viewers, mobyle-workflows +Description: Web portal that provides web forms for command-line software. + Mobyle is a framework and web portal specifically aimed at the integration of + bioinformatics software and databanks. It generates a web interface from an xml + description for command-line based tools. + It can submit jobs locally or using DRM systems. + +Package: mobyle-utils +Architecture: any +Depends: ${misc:Depends},${shlibs:Depends} +Description: binary tools used by Mobyle + Binary tools used by the Mobyle web portal to manage + jobs. Added: trunk/packages/mobyle/mobyle/trunk/debian/copyright =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/copyright (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/copyright 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,123 @@ +Format: http://dep.debian.net/deps/dep5 +Upstream-Name: mobyle +Source: https://projets.pasteur.fr/projects/show/mobyle + +Files: * +Copyright: 2011 Herve Menager <[email protected]> + 2011 Bertrand Néron <[email protected]> + 2011 Nicolas Joly <[email protected]> + 2011 Corinne Maufrais <[email protected]> + 2011 Sandrine Larroudé <[email protected]> + 2011 Pierre Tufféry <[email protected]> + 2011 Catherine Letondal <[email protected]> + 2011 Olivier Sallou <[email protected]> +License: GPL-2+ + This package is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + . + This package is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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See the + GNU General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/> + . + On Debian systems, the complete text of the GNU General + Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". + Added: trunk/packages/mobyle/mobyle/trunk/debian/docs =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/docs (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/docs 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,3 @@ +Doc/Admin/configuration_guide.pdf +Doc/Admin/execution_systems_guide.pdf +Doc/service_description_guide.pdf Added: trunk/packages/mobyle/mobyle/trunk/debian/get-orig-source =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/get-orig-source (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/get-orig-source 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,12 @@ +#!/bin/bash + +set -e + +PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` +VERSION=`uscan --verbose --force-download | + grep "Newest version on remote site is .* local version is .*" | + head -n 1 | + sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"` + +mkdir -p ../tarballs + Property changes on: trunk/packages/mobyle/mobyle/trunk/debian/get-orig-source ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/mobyle/mobyle/trunk/debian/mobyle-utils.dirs =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/mobyle-utils.dirs (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/mobyle-utils.dirs 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1 @@ +usr/bin Added: trunk/packages/mobyle/mobyle/trunk/debian/mobyle-utils.links =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/mobyle-utils.links (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/mobyle-utils.links 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1 @@ +usr/bin/mobyle-setsid usr/share/mobyle/core/Tools/setsid Added: trunk/packages/mobyle/mobyle/trunk/debian/mobyle.apache2 =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/mobyle.apache2 (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/mobyle.apache2 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,37 @@ + + Alias /mobyle /usr/share/mobyle/htdocs + + RewriteEngine on + #Support v0.97 URLs + RewriteCond %{REQUEST_URI} ^/cgi-bin/mobyle/portal.py + RewriteCond %{QUERY_STRING} form=(.*) + RewriteRule .* /cgi-bin/mobyle/portal.py?#forms::%1 [NE,R,L] + #Support v0.97 URLs + RewriteCond %{REQUEST_URI} ^/cgi-bin/mobyle/portal.py + RewriteCond %{QUERY_STRING} jobs=http://(.*)/(.*)/(.*)/(.*)/(.*) + RewriteRule .* /cgi-bin/mobyle/portal.py?#jobs::%4.%5 [NE,R,L] + + RewriteCond %{REQUEST_URI} ^/mobyle/data/jobs(\.*) + RewriteCond %{QUERY_STRING} ^save$ + RewriteRule (.*)/([^/]+)$ $1/$2 [E=SAVEDFILENAME:$2] + Header set Content-Disposition "attachment; filename=\"%{SAVEDFILENAME}e\"" env=SAVEDFILENAME + + + <Directory "/usr/lib/cgi-bin/mobyle"> + Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch + AllowOverride None + Options FollowSymLinks + Order allow,deny + Allow from all + SetEnv MOBYLEHOME /usr/share/mobyle/core + AddDefaultCharset ISO-8859-1 + </Directory> + + <Directory "/usr/share/mobyle/htdocs"> + Options -Indexes FollowSymLinks MultiViews + AllowOverride None + Order allow,deny + allow from all + </Directory> + + Added: trunk/packages/mobyle/mobyle/trunk/debian/mobyle.dirs =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/mobyle.dirs (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/mobyle.dirs 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,6 @@ +var/lib/mobyle +var/log/mobyle +usr/share/doc/mobyle +etc/mobyle +etc/mobyle/CustomClasses +etc/apache2/conf.d Added: trunk/packages/mobyle/mobyle/trunk/debian/mobyle.links =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/mobyle.links (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/mobyle.links 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,7 @@ +usr/share/javascript/scriptaculous/builder.js usr/share/mobyle/htdocs/portal/js/builder.js +usr/share/javascript/scriptaculous/effects.js usr/share/mobyle/htdocs/portal/js/effects.js +usr/share/javascript/scriptaculous/scriptaculous.js usr/share/mobyle/htdocs/portal/js/scriptaculous.js +usr/share/javascript/jquery/jquery.min/js usr/share/mobyle/htdocs/portal/js/openid/jquery-1.3.2.js +usr/share/javascript/prototype/prototype.js usr/share/mobyle/htdocs/portal/js/prototype-1.7.js +etc/mobyle/Config.py usr/share/mobyle/core/Local/Config/Config.py +etc/mobyle/CustomClasses/__init__.py usr/share/mobyle/core/Local/CustomClasses/__init__.py Added: trunk/packages/mobyle/mobyle/trunk/debian/patches/change_mobylehome =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/patches/change_mobylehome (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/patches/change_mobylehome 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,17 @@ +Author: Olivier Sallou <[email protected]> +Description: Change the Mobyle path in generated path to fit to Debian paths +Last-Update: 2011-08-09 +--- a/setup.py ++++ b/setup.py +@@ -120,9 +120,9 @@ + l = f.readline() + if not l: break + if mob and l == 'MOBYLEHOME = None\n': +- l = l.replace('None', "'"+mob+"'", 1) ++ l = l.replace('None', "'debian/mobyle/usr/share/mobyle/core'", 1) + if htm and l == 'MOBYLEHTDOCS = None\n': +- l = l.replace('None', "'"+htm+"'", 1) ++ l = l.replace('None', "'debian/mobyle/usr/share/mobyle/htdocs'", 1) + g.write(l) + g.close() + f.close() Added: trunk/packages/mobyle/mobyle/trunk/debian/patches/defaultconfig =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/patches/defaultconfig (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/patches/defaultconfig 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,30 @@ +--- a/Example/Local/Config/Config.template.py ++++ b/Example/Local/Config/Config.template.py +@@ -10,13 +10,13 @@ + + + # the root url of mobyle +-ROOT_URL = "http://mydomain.fr:port"; ++ROOT_URL = "http://localhost"; + + #base project url for mobyle cgis = ROOT_URL + CGI_PREFIX +-CGI_PREFIX = 'cgi-bin/mobyle/xxxxx' ++CGI_PREFIX = 'cgi-bin/mobyle' + + #base project url for mobyle htdocs = ROOT_URL + HTDOCS_PREFIX +-HTDOCS_PREFIX = 'mobyle/xxxxx' ++HTDOCS_PREFIX = 'mobyle' + + ######### + # # +@@ -94,8 +94,8 @@ + from Mobyle.Converter import * + + DATA_CONVERTER={ +- 'Sequence': [ squizz_sequence('/path/to/squizz') ] , +- 'Alignment': [ squizz_alignment('/path/to/squizz')] ++ 'Sequence': [ squizz_sequence('/usr/bin/squizz') ] , ++ 'Alignment': [ squizz_alignment('/usr/bin/squizz')] + } + + Added: trunk/packages/mobyle/mobyle/trunk/debian/patches/series =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/patches/series (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/patches/series 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,2 @@ +change_mobylehome +defaultconfig Added: trunk/packages/mobyle/mobyle/trunk/debian/postinst =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/postinst (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/postinst 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,44 @@ +#!/bin/sh + +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 [ ! -e /usr/share/mobyle/htdocs/data ] ; then + ln -s /var/lib/mobyle/data /usr/share/mobyle/htdocs/data + fi + chown -R www-data:www-data /var/log/mobyle + chown -R www-data:www-data /var/lib/mobyle + a2enmod rewrite + a2enmod headers + service apache2 restart + ;; + + 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 Added: trunk/packages/mobyle/mobyle/trunk/debian/rules =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/rules (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/rules 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,36 @@ +#!/usr/bin/make -f + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +%: + dh $@ + +override_dh_auto_build: + # Nothing to do + +override_dh_auto_install: + python setup.py install --install-cgis=debian/mobyle/usr/lib/cgi-bin/mobyle --install-htdocs=debian/mobyle/usr/share/mobyle/htdocs --install-core=debian/mobyle/usr/share/mobyle/core + mv debian/mobyle/usr/share/mobyle/htdocs/data debian/mobyle/var/lib/mobyle/ + rm -f debian/mobyle/usr/share/mobyle/htdocs/portal/js/scriptaculous.js + rm -f debian/mobyle/usr/share/mobyle/htdocs/portal/js/effects.js + rm -f debian/mobyle/usr/share/mobyle/htdocs/portal/js/builder.js + rm -f debian/mobyle/usr/share/mobyle/htdocs/portal/js/openid/jquery*.js + rm -f debian/mobyle/usr/share/mobyle/htdocs/portal/js/prototype*.js + rm -rf debian/mobyle/usr/share/mobyle/core/Doc + rm -rf debian/mobyle/usr/share/mobyle/core/Services/Programs + rm -rf debian/mobyle/usr/share/mobyle/core/Services/Viewers + rm -rf debian/mobyle/usr/share/mobyle/core/Services/Workflows +# cp -R Doc/* debian/mobyle/usr/share/doc/mobyle/ + cp debian/mobyle/usr/share/mobyle/core/Example/Local/Config/Config.template.py debian/mobyle/etc/mobyle/Config.py + cp debian/mobyle/usr/share/mobyle/core/Example/Local/CustomClasses/__init__.py debian/mobyle/etc/mobyle/CustomClasses/__init__.py + cp debian/mobyle.apache2 debian/mobyle/etc/apache2/conf.d/mobyle + find debian/mobyle -name *.html | xargs chmod 644 + find debian/mobyle -name *.xml | xargs chmod 644 + mv debian/mobyle/usr/share/mobyle/core/Tools/setsid debian/mobyle-utils/usr/bin/mobyle-setsid + + + + +get-orig-source: + bash debian/get-orig-source Property changes on: trunk/packages/mobyle/mobyle/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/mobyle/mobyle/trunk/debian/source/format =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/source/format (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/source/format 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/mobyle/mobyle/trunk/debian/watch =================================================================== --- trunk/packages/mobyle/mobyle/trunk/debian/watch (rev 0) +++ trunk/packages/mobyle/mobyle/trunk/debian/watch 2011-08-10 07:01:49 UTC (rev 7401) @@ -0,0 +1,3 @@ +version=3 + +opts=passive,filenamemangle=s/Mobyle/mobyle/ ftp://ftp.pasteur.fr/pub/gensoft/projects/mobyle/Mobyle-(\d+\.\d+\.\d+)\.tar\.gz debian uupdate _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
