[med-svn] [mobyle] 02/03: Add debian/ dir (svn2git failed and thus we simply lost history of svn)
Andreas Tille
tille at debian.org
Fri May 20 20:52:12 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository mobyle.
commit 5898834e4c236bef452c47267900149da6a78fa5
Author: Andreas Tille <tille at debian.org>
Date: Fri May 20 22:44:02 2016 +0200
Add debian/ dir (svn2git failed and thus we simply lost history of svn)
---
debian/README.Debian | 6 ++
debian/README.Silk | 23 ++++++
debian/README.source | 24 ++++++
debian/changelog | 126 ++++++++++++++++++++++++++++++
debian/compat | 1 +
debian/control | 67 ++++++++++++++++
debian/copyright | 160 +++++++++++++++++++++++++++++++++++++++
debian/docs | 5 ++
debian/get-orig-source | 36 +++++++++
debian/mobyle-utils.dirs | 1 +
debian/mobyle-utils.links | 1 +
debian/mobyle.1 | 29 +++++++
debian/mobyle.apache2 | 1 +
debian/mobyle.conf | 35 +++++++++
debian/mobyle.dirs | 10 +++
debian/mobyle.doc-base | 8 ++
debian/mobyle.links | 19 +++++
debian/mobyle.lintian-overrides | 1 +
debian/mobyle.manpages | 1 +
debian/patches/change_mobylehome | 17 +++++
debian/patches/defaultconfig | 48 ++++++++++++
debian/patches/mayhem.patch | 25 ++++++
debian/patches/series | 3 +
debian/postinst | 44 +++++++++++
debian/postrm | 22 ++++++
debian/rules | 45 +++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++
debian/watch | 3 +
29 files changed, 774 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..cd60235
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,6 @@
+To access the web portal, one should connect to http://localhost/cgi-bin/mobyle/portal.py
+
+Release 1.0.4 introduce a possible break in previous xml description.
+For more info: https://projets.pasteur.fr/repositories/entry/mobyle/tags/release_1_0_4/UPDATE?rev=3969
+
+Release 1.0.6 requires a mobyle-programs update to version 4.0. Those programs files are incompatible, and user XML files may need an update on issimple attribute usage (see UPDATE). To upgrade, remove package mobyle-programs, upgrade mobyle, then install mobyle-programs.
diff --git a/debian/README.Silk b/debian/README.Silk
new file mode 100644
index 0000000..7ed556d
--- /dev/null
+++ b/debian/README.Silk
@@ -0,0 +1,23 @@
+Silk Icons (http://www.famfamfam.com/lab/icons/silk/)
+
+“Silk” is a smooth, free icon set, containing over 700 16-by-16 pixel icons in
+strokably-soft PNG format. Containing a large variety of icons, you're sure to
+find something that tickles your fancy. And all for a low low price of $0.00.
+You can't say fairer than that.
+
+License
+
+I also love to hear of my work being used, feel encouraged to send an email
+with a link or screenshot of the icons in their new home to mjames at gmail dot
+com. This work is licensed under a Creative Commons Attribution 2.5 License.
+This means you may use it for any purpose, and make any changes you like. All I
+ask is that you include a link back to this page in your credits (although a
+giant link on every page of your website really isn't needed, contact me to
+discuss specifics).
+
+The icons can also be used under Creative Commons Attribution 3.0 License (Hi
+Debian folks!) with the following requirements:
+
+ As an author, I would appreciate a reference to my authorship of the Silk
+ icon set contents within a readme file or equivalent documentation for the
+ software which includes the set or a subset of the icons contained within.
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..cfee5f9
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,24 @@
+Mobyle needs to be downloaded with get-orig-source.
+Some copyright files need to be removed from upstream source (no impact on software).
+Other files are removed at the same time because those are available in debian packages (javascript,fonts...)
+
+Lintian warnings:
+
+Directories are present for use by user to place his programs (symlink from /var/lib)
+
+I: mobyle: package-contains-empty-directory usr/share/mobyle/core/Local/Services/Programs/
+I: mobyle: package-contains-empty-directory usr/share/mobyle/core/Local/Services/Viewers/
+I: mobyle: package-contains-empty-directory usr/share/mobyle/core/Local/Services/Workflows/
+I: mobyle: package-contains-empty-directory usr/share/mobyle/core/Local/Services/Tutorials/
+
+mobyle-setid is a small C program used by mobyle internally which explains it is not have a
+ nice description nor man page.
+
+I: mobyle-utils: extended-description-is-probably-too-short
+W: mobyle-utils: binary-without-manpage usr/bin/mobyle-setsid
+
+
+
+1 lintian error "privacy-breach" is overriden because:
+ - this is not AdSense but Google analytics which is used
+ - this option is not activated by default but by user configuration
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..e8fe6b1
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,126 @@
+mobyle (1.5.3+dfsg-3) unstable; urgency=medium
+
+ [ Mattia Rizzolo ]
+ * Remove dependency on python-support, and parametrize the python dependency
+ with ${python:Depends}, Build-Dep on dh-python.
+ Closes: #808166
+
+ [ Andreas Tille ]
+ * Add myself to Uploaders
+ * cme fix dpkg-control
+ * more verbose description for mobile-utils
+ * Fix mayhem issue
+ Closes: #716279
+ * Prevent duplicate changelogs
+ * Fix permission of *.xsl files
+
+ -- Andreas Tille <tille at debian.org> Wed, 16 Dec 2015 22:11:41 +0100
+
+mobyle (1.5.3+dfsg-2) unstable; urgency=medium
+
+ * d/control: set jing as Recommends, jing is not mandatory but only
+ useful for XML schema validation
+
+ -- Olivier Sallou <osallou at debian.org> Sun, 30 Nov 2014 12:51:07 +0100
+
+mobyle (1.5.3+dfsg-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 29 Apr 2014 08:22:48 +0200
+
+mobyle (1.5.1+dfsg-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 30 Jul 2013 16:01:45 +0200
+
+mobyle (1.5.0+dfsg-2) unstable; urgency=low
+
+ * Transition to Apache 2.4 (Closes: #669884).
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 31 May 2013 13:11:20 +0200
+
+mobyle (1.5.0+dfsg-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Mon, 18 Feb 2013 12:11:44 +0100
+
+mobyle (1.0.7+dfsg-1) unstable; urgency=low
+
+ [ Olivier Sallou ]
+ * New upstream release
+ * debian/get-orig-source: Normalised versioning (~dfsg -> +dfsg)
+
+ [ Andreas Tille ]
+ * debian/copyright:
+ - DEP5
+ - Add Files-Excluded to document what was removed from original source
+ * debian/watch: Normalised versioning (~dfsg -> +dfsg)
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 04 Sep 2012 13:27:00 +0200
+
+mobyle (1.0.6~dfsg-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Mon, 25 Jun 2012 15:55:39 +0200
+
+mobyle (1.0.5~dfsg-2) unstable; urgency=low
+
+ * Add postrm for clean purge.
+
+ -- Olivier Sallou <osallou at debian.org> Sun, 03 Jun 2012 13:36:48 +0200
+
+mobyle (1.0.5~dfsg-1) unstable; urgency=low
+
+ * New upstream release
+ * debian/patches/defaultconfig: add phylip binary path
+ * debian/control: remove some recommends
+ [ Andreas Tille ]
+ * debian/upstream: Added citations
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 22 May 2012 17:53:24 +0200
+
+mobyle (1.0.4~dfsg-3) unstable; urgency=low
+
+ * Use invoke-rc.d instead of service command to restart
+ apache as per Debian policy (Closes: #656078)
+ * Remove zx compression
+ * Add doc-base
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Mon, 16 Jan 2012 11:43:31 +0100
+
+mobyle (1.0.4~dfsg-2) unstable; urgency=low
+
+ * Add missing dep on python-pygraphviz for workflows
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Tue, 13 Dec 2011 13:48:42 +0100
+
+mobyle (1.0.4~dfsg-1) unstable; urgency=low
+
+ * New upstream version.
+ - Possible break in previous xml program description,
+ see README.Debian file for more info
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Wed, 07 Dec 2011 17:20:09 +0100
+
+mobyle (1.0.3~dfsg-1) unstable; urgency=low
+
+ * New upstream release (bug fixes)
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Wed, 02 Nov 2011 12:08:19 +0100
+
+mobyle (1.0.2~dfsg-2) unstable; urgency=low
+
+ * debian/rules : Thanks to A. Ucko
+ - fix issue when building arch depandant only package (Closes: #644277)
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Wed, 05 Oct 2011 13:35:00 +0900
+
+mobyle (1.0.2~dfsg-1) unstable; urgency=low
+
+ * Initial release (Closes: #637230)
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Mon, 03 Oct 2011 12:56:44 +0900
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..2255429
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,67 @@
+Source: mobyle
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>,
+ Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ python,
+ python-simpletal,
+ python-simplejson,
+ python-imaging,
+ python-lxml,
+ dh-apache2,
+ apache2-dev,
+ dh-python
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mobyle/mobyle/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mobyle/mobyle/trunk/
+Homepage: https://projets.pasteur.fr/projects/show/mobyle
+X-Python-Version: >= 2.5
+
+Package: mobyle
+Architecture: all
+Depends: ${misc:Depends},
+ ${python:Depends},
+ apache2 (>= 2.4) | httpd-cgi,
+ libjs-scriptaculous,
+ libjs-jquery,
+ libjs-prototype,
+ mobyle-utils,
+ python-biopython,
+ python-imaging,
+ python-lxml,
+ python-pygraphviz,
+ python-simplejson,
+ python-simpletal,
+ python-simpletal (<< 5.0~),
+ squizz (>= 0.99b+dfsg),
+ ttf-bitstream-vera
+Recommends: mobyle-programs,
+ mobyle-tutorials,
+ ${misc:Recommends},
+ jing
+Suggests: python-openid,
+ python-dnspython
+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.
+ .
+ This package will restart Apache after enabling the ‘rewrite’ and ‘headers’
+ modules.
+
+Package: mobyle-utils
+Architecture: any
+Depends: ${misc:Depends},
+ ${shlibs:Depends},
+ ${python:Depends}
+Description: binary tools used by Mobyle
+ 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.
+ .
+ Binary tools used by the Mobyle web portal to manage
+ jobs.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..a0b4cdf
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,160 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: mobyle
+Source: https://projets.pasteur.fr/projects/show/mobyle
+Files-Excluded:
+ Src/Mobyle/Test/Converter/DataSequences/sequence.SWISSPROT
+ Src/Portal/htdocs/MobylePortal/js/openid/jquery-1.3.2.min.js
+ Src/Portal/htdocs/MobylePortal/js/scriptaculous.js
+ Src/Portal/htdocs/MobylePortal/js/builder.js
+ Src/Portal/htdocs/MobylePortal/js/effects.js
+ Src/Portal/htdocs/MobylePortal/js/prototype-1.7.js
+ Src/Mobyle/Captcha/data/fonts/vera
+
+Files: *
+Copyright: 2011 Herve Menager <hmenager at pasteur.fr>
+ 2011 Bertrand Néron <bneron at pasteur.fr>
+ 2011 Nicolas Joly <njoly at pasteur.fr>
+ 2011 Corinne Maufrais <maufrais at pasteur.fr>
+ 2011 Sandrine Larroudé <slarroud at pasteur.fr>
+ 2011 Pierre Tufféry <pierre.tuffery at univ-paris-diderot.fr>
+ 2011 Catherine Letondal <letondal at pasteur.fr>
+ 2011 Olivier Sallou <olivier.sallou at irisa.fr>
+License: GPL-2+
+
+Files: Src/Portal/htdocs/MobylePortal/js/blank.html
+ Src/Portal/htdocs/MobylePortal/js/rsh.js
+Copyright: 2007 Brian Dillard <bdillard at pathf.com>
+ 2007 Brad Neuberg
+License: MIT
+
+Files: Src/Portal/htdocs/MobylePortal/images/*
+Copyright: 2011 Mark James
+License: CC-BY-SA-3.0
+Source: http://www.famfamfam.com/lab/icons/silk/
+Coment: debian/README.Silk created according to the following comment on Upstream website.
+ The icons can also be used under Creative Commons Attribution 3.0 License (Hi
+ Debian folks!) with the following requirements:
+ .
+ As an author, I would appreciate a reference to my authorship of the Silk
+ icon set contents within a readme file or equivalent documentation for the
+ software which includes the set or a subset of the icons contained within.
+
+Files: Tools/validation/iso_*.xsl
+Source: http://www.schematron.com/implementation.html
+Copyright: © 2001, 2006 Rick Jelliffe and Academia Sinica Computing Center, Taiwan
+License: zlib
+
+Files: Src/Mobyle/Captcha/*
+Source: http://releases.navi.cx/pycaptcha/
+Copyright: 2004 Micah Dowty
+License: MIT
+
+Files: debian/*
+Copyright: 2011 Olivier Sallou <olivier.sallou at irisa.fr>
+License: GPL-2+
+
+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. 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".
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
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+ If any provision of this License is invalid or unenforceable under applicable law, it shall not affect the validity or enforceability of the remainder of the terms of this License, and without further action by the parties to this agreement, such provision shall be reformed to the minimum extent necessary to make such provision valid and enforceable.
+ No term or provision of this License shall be deemed waived and no breach consented to unless such waiver or consent shall be in writing and signed by the party to be charged with such waiver or consent.
+ This License constitutes the entire agreement between the parties with respect to the Work licensed here. There are no understandings, agreements or representations with respect to the Work not specified here. Licensor shall not be bound by any additional provisions that may appear in any communication from You. This License may not be modified without the mutual written agreement of the Licensor and You.
+ The rights granted under, and the subject matter referenced, in this License were drafted utilizing the terminology of the Berne Convention for the Protection of Literary and Artistic Works (as amended on September 28, 1979), the Rome Convention of 1961, the WIPO Copyright Treaty of 1996, the WIPO Performances and Phonograms Treaty of 1996 and the Universal Copyright Convention (as revised on July 24, 1971). These rights and subject matter take effect in the relevant jurisdiction in whi [...]
+
+License: zlib
+ This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software.
+ .
+ Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions:
+ .
+ 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required.
+ .
+ 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software.
+ .
+ 3. This notice may not be removed or altered from any source distribution.
+
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..d32164d
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,5 @@
+Doc/Admin/configuration_guide.pdf
+Doc/Admin/execution_systems_guide.pdf
+Doc/service_description_guide.pdf
+NEWS
+UPDATE
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..d4fc25b
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,36 @@
+#!/bin/bash
+
+set -e
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download --no-symlink |
+ 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
+
+cd ../tarballs
+
+UTAR="${PKG}-${VERSION}.tar.gz"
+mv ../${UTAR} .
+tar -xzf ${UTAR}
+
+mv Mobyle-${VERSION} $PKG-${VERSION}+dfsg.orig # .orig is requested by Developers Reference 3.4.4 §6.7.8.2
+
+cd $PKG-${VERSION}+dfsg.orig
+# remove license issue file
+rm Src/Mobyle/Test/Converter/DataSequences/sequence.SWISSPROT
+# remove unnecessary files, standard packages will be used
+rm Src/Portal/htdocs/MobylePortal/js/openid/jquery-1.3.2.min.js
+rm Src/Portal/htdocs/MobylePortal/js/scriptaculous.js
+rm Src/Portal/htdocs/MobylePortal/js/builder.js
+rm Src/Portal/htdocs/MobylePortal/js/effects.js
+rm Src/Portal/htdocs/MobylePortal/js/prototype-1.7.js
+rm -rf Src/Mobyle/Captcha/data/fonts/vera
+cd ..
+
+BZIP2="--best" tar -cjf ${PKG}_${VERSION}+dfsg.orig.tar.bz2 ${PKG}-${VERSION}+dfsg.orig
+rm -rf ${PKG}-${VERSION}+dfsg.orig
+
+rm ${UTAR}
diff --git a/debian/mobyle-utils.dirs b/debian/mobyle-utils.dirs
new file mode 100644
index 0000000..e772481
--- /dev/null
+++ b/debian/mobyle-utils.dirs
@@ -0,0 +1 @@
+usr/bin
diff --git a/debian/mobyle-utils.links b/debian/mobyle-utils.links
new file mode 100644
index 0000000..bd69374
--- /dev/null
+++ b/debian/mobyle-utils.links
@@ -0,0 +1 @@
+usr/bin/mobyle-setsid usr/share/mobyle/core/Tools/setsid
diff --git a/debian/mobyle.1 b/debian/mobyle.1
new file mode 100644
index 0000000..e023e6f
--- /dev/null
+++ b/debian/mobyle.1
@@ -0,0 +1,29 @@
+.TH mobyle 1 "September 14, 2011" "version 1.0" "USER COMMANDS"
+.SH NAME
+mobyle \- Framework and web portal specifically aimed at the integration of bioinformatics software and databanks.
+.SH SYNOPSIS
+.B mobyle
+Portal is accessible at http://localhost/cgi-bin/mobyle/portal.py
+.SH CONFIGURATION
+ Configuration of the portal is available in /etc/mobyle/Config.py.
+ Some administrator and user docs are available with the package.
+ By default, anonymous access is authorized with captcha support and
+ jobs are executed in local mode.
+
+ Custom classes can be specified in /etc/mobyle/CustomClasses.py
+.PP
+.SH TUTORIAL
+Documentation details user and admin usage. A step-by-step
+ tutorial is available on the portal. To use this online tutorial,
+ the package mobyle-programs is required.
+.PP
+.SH PROGRAMS
+ Programs, viewers and worflows descriptors are located in /var/lib/mobyle/programs.
+ Program environments are in /etc/mobyle/programs/.
+Package mobyle-programs offer a set of preconfigured programs based on emboss, phylip etc...
+.PP
+.SH TOOLS
+ Tools to (un)deploy programs, viewers, ... are in /usr/share/mobyle/core/Tools.
+.SH AUTHOR
+Olivier Sallou (olivier.sallou (at) irisa.fr)
+
diff --git a/debian/mobyle.apache2 b/debian/mobyle.apache2
new file mode 100644
index 0000000..131e9e2
--- /dev/null
+++ b/debian/mobyle.apache2
@@ -0,0 +1 @@
+conf debian/mobyle.conf
diff --git a/debian/mobyle.conf b/debian/mobyle.conf
new file mode 100644
index 0000000..1577c0e
--- /dev/null
+++ b/debian/mobyle.conf
@@ -0,0 +1,35 @@
+
+ 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
+ Require all granted
+ SetEnv MOBYLEHOME /usr/share/mobyle/core
+ AddDefaultCharset ISO-8859-1
+ </Directory>
+
+ <Directory "/usr/share/mobyle/htdocs">
+ Options -Indexes +FollowSymLinks +MultiViews
+ AllowOverride None
+ Require all granted
+ </Directory>
+
+
diff --git a/debian/mobyle.dirs b/debian/mobyle.dirs
new file mode 100644
index 0000000..779181d
--- /dev/null
+++ b/debian/mobyle.dirs
@@ -0,0 +1,10 @@
+var/lib/mobyle
+var/lib/mobyle/programs
+var/lib/mobyle/viewers
+var/lib/mobyle/workflows
+var/lib/mobyle/tutorials
+var/log/mobyle
+usr/share/doc/mobyle
+etc/mobyle
+etc/mobyle/CustomClasses
+etc/apache2/conf.d
diff --git a/debian/mobyle.doc-base b/debian/mobyle.doc-base
new file mode 100644
index 0000000..c30b15a
--- /dev/null
+++ b/debian/mobyle.doc-base
@@ -0,0 +1,8 @@
+Document: mobyle
+Title: Mobyle Administrator guides
+Author: Mobyle team
+Abstract: Configuration and Mobyle service creation
+Section: Help/HOWTO
+
+Format: PDF
+Files: /usr/share/doc/mobyle/*_guide.pdf.gz
diff --git a/debian/mobyle.links b/debian/mobyle.links
new file mode 100644
index 0000000..0e2f155
--- /dev/null
+++ b/debian/mobyle.links
@@ -0,0 +1,19 @@
+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
+usr/share/java/jing.jar usr/share/mobyle/core/Tools/validation/jing/jing.jar
+usr/share/java/isorelax.jar usr/share/mobyle/core/Tools/validation/jing/isorelax.jar
+usr/share/java/saxon.jar usr/share/mobyle/core/Tools/validation/jing/saxon.jar
+usr/share/java/xercesImpl.jar usr/share/mobyle/core/Tools/validation/jing/xercesImpl.jar
+usr/share/java/xml-apis.jar usr/share/mobyle/core/Tools/validation/jing/xml-apis.jar
+usr/share/fonts/truetype/ttf-bitstream-vera usr/share/mobyle/core/Src/Mobyle/Captcha/data/fonts/vera
+var/lib/mobyle/data usr/share/mobyle/htdocs/data
+etc/mobyle/announcement.txt usr/share/mobyle/htdocs/portal/html/announcement.txt
+var/lib/mobyle/programs usr/share/mobyle/core/Services/Programs
+var/lib/mobyle/viewers usr/share/mobyle/core/Services/Viewers
+var/lib/mobyle/workflows usr/share/mobyle/core/Services/Workflows
+var/lib/mobyle/tutorials usr/share/mobyle/core/Services/Tutorials
diff --git a/debian/mobyle.lintian-overrides b/debian/mobyle.lintian-overrides
new file mode 100644
index 0000000..b29de03
--- /dev/null
+++ b/debian/mobyle.lintian-overrides
@@ -0,0 +1 @@
+mobyle: privacy-breach-google-adsense usr/share/mobyle/htdocs/portal/js/mobyle_ga.js
diff --git a/debian/mobyle.manpages b/debian/mobyle.manpages
new file mode 100644
index 0000000..7b8ee49
--- /dev/null
+++ b/debian/mobyle.manpages
@@ -0,0 +1 @@
+debian/mobyle.1
diff --git a/debian/patches/change_mobylehome b/debian/patches/change_mobylehome
new file mode 100644
index 0000000..d1dea87
--- /dev/null
+++ b/debian/patches/change_mobylehome
@@ -0,0 +1,17 @@
+Author: Olivier Sallou <olivier.sallou at irisa.fr>
+Description: Change the Mobyle path in generated path to fit to Debian paths
+Last-Update: 2011-08-09
+--- a/setup.py
++++ b/setup.py
+@@ -148,9 +148,9 @@
+ 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()
diff --git a/debian/patches/defaultconfig b/debian/patches/defaultconfig
new file mode 100644
index 0000000..db1e623
--- /dev/null
+++ b/debian/patches/defaultconfig
@@ -0,0 +1,48 @@
+Author: Olivier Sallou <olivier.sallou at irisa.fr>
+Description: Set default config for ready-to-run app
+Last-Update: 2011-08-09
+--- a/Example/Local/Config/Config.template.py
++++ b/Example/Local/Config/Config.template.py
+@@ -12,13 +12,13 @@
+ # the root url of mobyle
+ # warning: do NOT include the port number if it is 80, it is useless
+ # and creates problems on the server
+-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'
+
+ #########
+ # #
+@@ -96,8 +96,14 @@
+ 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'),
++ fasta_phyml(None),
++ phylipi_phyml(None),
++ phylips_phyml(None),
++ clustal_phyml(None),
++ nexus_phyml(None),
++ stockholm_phyml(None)]
+ }
+
+
+@@ -152,7 +158,7 @@
+ ## each element must be a valid path
+ ## the element order is kept to build the final PATH ( the binary path is add before the canonical PATH )
+
+-BINARY_PATH = ["/usr/local/bin"]
++BINARY_PATH = ["/usr/local/bin","/usr/lib/phylip/bin"]
+
+
+ #DATABANKS_CONFIG = {
diff --git a/debian/patches/mayhem.patch b/debian/patches/mayhem.patch
new file mode 100644
index 0000000..dd50bfe
--- /dev/null
+++ b/debian/patches/mayhem.patch
@@ -0,0 +1,25 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 16 Dec 2015 21:49:59 +0100
+Bugs-Debian: https://bugs.debian.org/716279
+Description: Fix mayhem issue
+
+--- a/Tools/setsid.c
++++ b/Tools/setsid.c
+@@ -1,4 +1,4 @@
+-
++#include <stdio.h>
+ #include <unistd.h>
+
+ int main(int argc, char **argv) {
+@@ -7,6 +7,10 @@ int main(int argc, char **argv) {
+ (void)setsid();
+
+ /* Execute the real command */
+- execvp(argv[1], argv+1);
++ if (argc > 1) {
++ execvp(argv[1], argv+1);
++ } else {
++ fprintf(stderr, "%s missing arguments\n", argv[0]);
++ }
+
+ return 1; }
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..aa08ede
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+change_mobylehome
+defaultconfig
+mayhem.patch
diff --git a/debian/postinst b/debian/postinst
new file mode 100644
index 0000000..b4ff396
--- /dev/null
+++ b/debian/postinst
@@ -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)
+ chown -R www-data:www-data /var/log/mobyle
+ chown -R www-data:www-data /var/lib/mobyle
+ if [ -e /usr/share/apache2/apache2-maintscript-helper ] ; then
+ . /usr/share/apache2/apache2-maintscript-helper
+ apache2_invoke enmod rewrite
+ apache2_invoke enmod headers
+ apache2_invoke enmod alias
+ 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
diff --git a/debian/postrm b/debian/postrm
new file mode 100644
index 0000000..d0185c7
--- /dev/null
+++ b/debian/postrm
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+set -e
+
+case "$1" in
+ purge|remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
+
+ if [ "$1" = "purge" ] ; then
+ rm -rf /var/log/mobyle
+ rm -rf /var/lib/mobyle
+ fi
+ ;;
+
+ *)
+ echo "postrm called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+
+#DEBHELPER#
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..586efd6
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,45 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@ --with python2 --with apache2
+
+override_dh_auto_build:
+ # Nothing to do
+
+get-orig-source:
+ bash debian/get-orig-source
+
+clean:
+ dh clean --with python2
+ rm -f debian/common-install-stamp
+
+debian/common-install-stamp:
+ 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
+ touch $@
+
+override_dh_auto_install-arch: debian/common-install-stamp
+ mv debian/mobyle/usr/share/mobyle/core/Tools/setsid debian/mobyle-utils/usr/bin/mobyle-setsid
+
+override_dh_auto_install-indep: debian/common-install-stamp
+ find debian/mobyle/usr/share/mobyle/core -type f | xargs sed -i "s/MOBYLEHOME = '.*'/MOBYLEHOME = '\/usr\/share\/mobyle\/core'/g"
+ find debian/mobyle/usr/lib/cgi-bin/mobyle -type f | xargs sed -i "s/MOBYLEHOME = '.*'/MOBYLEHOME = '\/usr\/share\/mobyle\/core'/g"
+ find debian/mobyle/usr/share/mobyle/core -type f | xargs sed -i "s/MOBYLEHTDOCS = '.*'/MOBYLEHTDOCS = '\/usr\/share\/mobyle\/htdocs'/g"
+ mv debian/mobyle/usr/share/mobyle/htdocs/data debian/mobyle/var/lib/mobyle/
+ rm -rf debian/mobyle/usr/share/mobyle/core/Doc
+ rm -f debian/mobyle/usr/share/mobyle/core/Src/Mobyle/Captcha/COPYING
+ 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
+ rm -rf debian/mobyle/usr/share/mobyle/core/Services/Tutorials
+ 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
+ find debian/mobyle -name *.html | xargs chmod 644
+ find debian/mobyle -name *.xml | xargs chmod 644
+ mv debian/mobyle/usr/share/mobyle/htdocs/portal/html/announcement.txt debian/mobyle/etc/mobyle/
+
+override_dh_fixperms:
+ dh_fixperms
+ find debian -name "*.xsl" -exec chmod -x \{\} \;
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..2a0df24
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Bertrand Neron and Herve Menager and Corinne Maufrais and Nicolas Joly and Julien Maupetit and Sebastien Letort and Sebastien Carrere and Pierre Tuffery and Catherine Letondal
+ Title: "Mobyle: a new full web bioinformatics framework"
+ Journal: Bioinformatics
+ Year: 2009
+ Volume: 25
+ Number: 22
+ Pages: 3005-11
+ DOI: 10.1093/bioinformatics/btp493
+ PMID: 19689959
+ URL: http://bioinformatics.oxfordjournals.org/content/25/22/3005.abstract
+ eprint: http://bioinformatics.oxfordjournals.org/content/25/22/3005.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..f71f9fc
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+opts=passive,filenamemangle=s/Mobyle/mobyle/,dversionmangle=s/\+dfsg// ftp://ftp.pasteur.fr/pub/gensoft/projects/mobyle/Mobyle-(\d+\.\d+\.\d+)\.tar\.gz
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