[med-svn] [obitools] 02/09: [svn-inject] Application des modifications Debian (1.1.16+dfsg-1) pour le tronc
Andreas Tille
tille at debian.org
Wed Dec 13 18:18:16 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository obitools.
commit 4e11f338b5cb5ecb1ccf56f7b77f30233146dd64
Author: Olivier Sallou <osallou at debian.org>
Date: Thu Apr 30 16:10:55 2015 +0000
[svn-inject] Application des modifications Debian (1.1.16+dfsg-1) pour le tronc
---
debian/README.Debian | 6 +
debian/README.source | 10 +
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 18 +
debian/copyright | 1033 +++++++++++++++++++++++++++++++++++
debian/docs | 3 +
debian/init.d.ex | 166 ++++++
debian/manpage.1.ex | 56 ++
debian/manpage.sgml.ex | 154 ++++++
debian/manpage.xml.ex | 291 ++++++++++
debian/menu.ex | 2 +
debian/obitools.cron.d.ex | 4 +
debian/obitools.default.ex | 10 +
debian/obitools.doc-base.EX | 20 +
debian/patches/fix_path_interpreter | 315 +++++++++++
debian/patches/series | 2 +
debian/patches/use_debian_libs | 82 +++
debian/postinst.ex | 39 ++
debian/postrm.ex | 37 ++
debian/preinst.ex | 35 ++
debian/prerm.ex | 38 ++
debian/python-obitools.doc-base | 9 +
debian/python-obitools.install | 1 +
debian/python-obitools.links | 3 +
debian/python-obitools.manpages | 1 +
debian/rules | 42 ++
debian/source/format | 1 +
debian/watch | 3 +
29 files changed, 2387 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..87af727
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,6 @@
+obitools for Debian
+-------------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- Olivier Sallou <osallou at debian.org> Thu, 30 Apr 2015 15:24:37 +0200
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..9fb2aba
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,10 @@
+obitools for Debian
+-------------------
+
+<this file describes information about the source package, see Debian policy
+manual section 4.14. You WILL either need to modify or delete this file>
+
+
+
+ -- Olivier Sallou <osallou at debian.org> Thu, 30 Apr 2015 15:24:37 +0200
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..2f9b5ff
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+obitools (1.1.16+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #783833)
+
+ -- Olivier Sallou <osallou at debian.org> Thu, 30 Apr 2015 15:24:37 +0200
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..f806cbf
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,18 @@
+Source: obitools
+Section: python
+Priority: optional
+Maintainer: Olivier Sallou <osallou at debian.org>
+Build-Depends: debhelper (>= 9), dh-python,
+ python-sphinx, cython, ipython, python-wheel
+Standards-Version: 3.9.6
+Homepage: https://pypi.python.org/pypi/OBITools
+#Vcs-Git: git://anonscm.debian.org/collab-maint/obitools.git
+#Vcs-Browser: http://anonscm.debian.org/?p=collab-maint/obitools.git;a=summary
+X-Python-Version: >= 2.7
+
+Package: python-obitools
+Architecture: amd64
+Depends: ${misc:Depends}, ${python:Depends}, ${shlibs:Depends},
+ ${sphinxdoc:Depends}, libjs-sphinxdoc
+Description: <insert up to 60 chars description>
+ <insert long description, indented with spaces>
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..165091c
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,1033 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: obitools
+Source: http://metabarcoding.org//obitools
+Files-Excluded:
+ distutils.ext/obidistutils/serenity/pip
+ build
+
+
+Files: src/obitools/SVGdraw.py
+Copyright: 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen)
+License: BSD
+ All rights reserved.
+ .
+ Redistribution and use in source and binary forms, with or without modification,
+ are permitted provided that the following conditions are met:
+ .
+ Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+ .
+ Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation and/or
+ other materials provided with the distribution.
+ .
+ Neither the name of the Stichting Farmaceutische Kengetallen nor the names of
+ its contributors may be used to endorse or promote products derived from this
+ software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: *
+Copyright: 2014 Eric Coissac <eric at coissac.eu>
+ 2014 Boyer F
+ 2014 Mercier C
+ 2014 Bonin A
+ 2014 Taberlet P
+License: CeCILL 2.1
+ CeCILL FREE SOFTWARE LICENSE AGREEMENT
+ .
+ Notice
+ .
+ This Agreement is a Free Software license agreement that is the result
+ of discussions between its authors in order to ensure compliance with
+ the two main principles guiding its drafting:
+ .
+ * firstly, compliance with the principles governing the distribution
+ of Free Software: access to source code, broad rights granted to
+ users,
+ * secondly, the election of a governing law, French law, with which
+ it is conformant, both as regards the law of torts and
+ intellectual property law, and the protection that it offers to
+ both authors and holders of the economic rights over software.
+ .
+ The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+ license are:
+ .
+ Commissariat à l'Energie Atomique - CEA, a public scientific, technical
+ and industrial research establishment, having its principal place of
+ business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
+ .
+ Centre National de la Recherche Scientifique - CNRS, a public scientific
+ and technological establishment, having its principal place of business
+ at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
+ .
+ Institut National de Recherche en Informatique et en Automatique -
+ INRIA, a public scientific and technological establishment, having its
+ principal place of business at Domaine de Voluceau, Rocquencourt, BP
+ 105, 78153 Le Chesnay cedex, France.
+ .
+ Preamble
+ .
+ The purpose of this Free Software license agreement is to grant users
+ the right to modify and redistribute the software governed by this
+ license within the framework of an open source distribution model.
+ .
+ The exercising of these rights is conditional upon certain obligations
+ for users so as to preserve this status for all subsequent redistributions.
+ .
+ In consideration of access to the source code and the rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors only have limited liability.
+ .
+ In this respect, the risks associated with loading, using, modifying
+ and/or developing or reproducing the software by the user are brought to
+ the user's attention, given its Free Software status, which may make it
+ complicated to use, with the result that its use is reserved for
+ developers and experienced professionals having in-depth computer
+ knowledge. Users are therefore encouraged to load and test the
+ suitability of the software as regards their requirements in conditions
+ enabling the security of their systems and/or data to be ensured and,
+ more generally, to use and operate it in the same conditions of
+ security. This Agreement may be freely reproduced and published,
+ provided it is not altered, and that no provisions are either added or
+ removed herefrom.
+ .
+ This Agreement may apply to any or all software for which the holder of
+ the economic rights decides to submit the use thereof to its provisions.
+ .
+ Article 1 - DEFINITIONS
+ .
+ For the purpose of this Agreement, when the following expressions
+ commence with a capital letter, they shall have the following meaning:
+ .
+ Agreement: means this license agreement, and its possible subsequent
+ versions and annexes.
+ .
+ Software: means the software in its Object Code and/or Source Code form
+ and, where applicable, its documentation, "as is" when the Licensee
+ accepts the Agreement.
+ .
+ Initial Software: means the Software in its Source Code and possibly its
+ Object Code form and, where applicable, its documentation, "as is" when
+ it is first distributed under the terms and conditions of the Agreement.
+ .
+ Modified Software: means the Software modified by at least one
+ Contribution.
+ .
+ Source Code: means all the Software's instructions and program lines to
+ which access is required so as to modify the Software.
+ .
+ Object Code: means the binary files originating from the compilation of
+ the Source Code.
+ .
+ Holder: means the holder(s) of the economic rights over the Initial
+ Software.
+ .
+ Licensee: means the Software user(s) having accepted the Agreement.
+ .
+ Contributor: means a Licensee having made at least one Contribution.
+ .
+ Licensor: means the Holder, or any other individual or legal entity, who
+ distributes the Software under the Agreement.
+ .
+ Contribution: means any or all modifications, corrections, translations,
+ adaptations and/or new functions integrated into the Software by any or
+ all Contributors, as well as any or all Internal Modules.
+ .
+ Module: means a set of sources files including their documentation that
+ enables supplementary functions or services in addition to those offered
+ by the Software.
+ .
+ External Module: means any or all Modules, not derived from the
+ Software, so that this Module and the Software run in separate address
+ spaces, with one calling the other when they are run.
+ .
+ Internal Module: means any or all Module, connected to the Software so
+ that they both execute in the same address space.
+ .
+ GNU GPL: means the GNU General Public License version 2 or any
+ subsequent version, as published by the Free Software Foundation Inc.
+ .
+ Parties: mean both the Licensee and the Licensor.
+ .
+ These expressions may be used both in singular and plural form.
+ .
+ Article 2 - PURPOSE
+ .
+ The purpose of the Agreement is the grant by the Licensor to the
+ Licensee of a non-exclusive, transferable and worldwide license for the
+ Software as set forth in Article 5 hereinafter for the whole term of the
+ protection granted by the rights over said Software.
+ .
+ Article 3 - ACCEPTANCE
+ .
+ 3.1 The Licensee shall be deemed as having accepted the terms and
+ conditions of this Agreement upon the occurrence of the first of the
+ following events:
+ .
+ * (i) loading the Software by any or all means, notably, by
+ downloading from a remote server, or by loading from a physical
+ medium;
+ * (ii) the first time the Licensee exercises any of the rights
+ granted hereunder.
+ .
+ 3.2 One copy of the Agreement, containing a notice relating to the
+ characteristics of the Software, to the limited warranty, and to the
+ fact that its use is restricted to experienced users has been provided
+ to the Licensee prior to its acceptance as set forth in Article 3.1
+ hereinabove, and the Licensee hereby acknowledges that it has read and
+ understood it.
+ .
+ Article 4 - EFFECTIVE DATE AND TERM
+ .
+ 4.1 EFFECTIVE DATE
+ .
+ The Agreement shall become effective on the date when it is accepted by
+ the Licensee as set forth in Article 3.1.
+ .
+ 4.2 TERM
+ .
+ The Agreement shall remain in force for the entire legal term of
+ protection of the economic rights over the Software.
+ .
+ Article 5 - SCOPE OF RIGHTS GRANTED
+ .
+ The Licensor hereby grants to the Licensee, who accepts, the following
+ rights over the Software for any or all use, and for the term of the
+ Agreement, on the basis of the terms and conditions set forth hereinafter.
+ .
+ Besides, if the Licensor owns or comes to own one or more patents
+ protecting all or part of the functions of the Software or of its
+ components, the Licensor undertakes not to enforce the rights granted by
+ these patents against successive Licensees using, exploiting or
+ modifying the Software. If these patents are transferred, the Licensor
+ undertakes to have the transferees subscribe to the obligations set
+ forth in this paragraph.
+ .
+ 5.1 RIGHT OF USE
+ .
+ The Licensee is authorized to use the Software, without any limitation
+ as to its fields of application, with it being hereinafter specified
+ that this comprises:
+ .
+ 1. permanent or temporary reproduction of all or part of the Software
+ by any or all means and in any or all form.
+ .
+ 2. loading, displaying, running, or storing the Software on any or
+ all medium.
+ .
+ 3. entitlement to observe, study or test its operation so as to
+ determine the ideas and principles behind any or all constituent
+ elements of said Software. This shall apply when the Licensee
+ carries out any or all loading, displaying, running, transmission
+ or storage operation as regards the Software, that it is entitled
+ to carry out hereunder.
+ .
+ 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+ .
+ The right to make Contributions includes the right to translate, adapt,
+ arrange, or make any or all modifications to the Software, and the right
+ to reproduce the resulting software.
+ .
+ The Licensee is authorized to make any or all Contributions to the
+ Software provided that it includes an explicit notice that it is the
+ author of said Contribution and indicates the date of the creation thereof.
+ .
+ 5.3 RIGHT OF DISTRIBUTION
+ .
+ In particular, the right of distribution includes the right to publish,
+ transmit and communicate the Software to the general public on any or
+ all medium, and by any or all means, and the right to market, either in
+ consideration of a fee, or free of charge, one or more copies of the
+ Software by any means.
+ .
+ The Licensee is further authorized to distribute copies of the modified
+ or unmodified Software to third parties according to the terms and
+ conditions set forth hereinafter.
+ .
+ 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+ .
+ The Licensee is authorized to distribute true copies of the Software in
+ Source Code or Object Code form, provided that said distribution
+ complies with all the provisions of the Agreement and is accompanied by:
+ .
+ 1. a copy of the Agreement,
+ .
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+ .
+ and that, in the event that only the Object Code of the Software is
+ redistributed, the Licensee allows future Licensees unhindered access to
+ the full Source Code of the Software by indicating how to access it, it
+ being understood that the additional cost of acquiring the Source Code
+ shall not exceed the cost of transferring the data.
+ .
+ 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+ .
+ When the Licensee makes a Contribution to the Software, the terms and
+ conditions for the distribution of the resulting Modified Software
+ become subject to all the provisions of this Agreement.
+ .
+ The Licensee is authorized to distribute the Modified Software, in
+ source code or object code form, provided that said distribution
+ complies with all the provisions of the Agreement and is accompanied by:
+ .
+ 1. a copy of the Agreement,
+ .
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+ .
+ and that, in the event that only the object code of the Modified
+ Software is redistributed, the Licensee allows future Licensees
+ unhindered access to the full source code of the Modified Software by
+ indicating how to access it, it being understood that the additional
+ cost of acquiring the source code shall not exceed the cost of
+ transferring the data.
+ .
+ 5.3.3 DISTRIBUTION OF EXTERNAL MODULES
+ .
+ When the Licensee has developed an External Module, the terms and
+ conditions of this Agreement do not apply to said External Module, that
+ may be distributed under a separate license agreement.
+ .
+ 5.3.4 COMPATIBILITY WITH THE GNU GPL
+ .
+ The Licensee can include a code that is subject to the provisions of one
+ of the versions of the GNU GPL in the Modified or unmodified Software,
+ and distribute that entire code under the terms of the same version of
+ the GNU GPL.
+ .
+ The Licensee can include the Modified or unmodified Software in a code
+ that is subject to the provisions of one of the versions of the GNU GPL,
+ and distribute that entire code under the terms of the same version of
+ the GNU GPL.
+ .
+ Article 6 - INTELLECTUAL PROPERTY
+ .
+ 6.1 OVER THE INITIAL SOFTWARE
+ .
+ The Holder owns the economic rights over the Initial Software. Any or
+ all use of the Initial Software is subject to compliance with the terms
+ and conditions under which the Holder has elected to distribute its work
+ and no one shall be entitled to modify the terms and conditions for the
+ distribution of said Initial Software.
+ .
+ The Holder undertakes that the Initial Software will remain ruled at
+ least by this Agreement, for the duration set forth in Article 4.2.
+ .
+ 6.2 OVER THE CONTRIBUTIONS
+ .
+ The Licensee who develops a Contribution is the owner of the
+ intellectual property rights over this Contribution as defined by
+ applicable law.
+ .
+ 6.3 OVER THE EXTERNAL MODULES
+ .
+ The Licensee who develops an External Module is the owner of the
+ intellectual property rights over this External Module as defined by
+ applicable law and is free to choose the type of agreement that shall
+ govern its distribution.
+ .
+ 6.4 JOINT PROVISIONS
+ .
+ The Licensee expressly undertakes:
+ .
+ 1. not to remove, or modify, in any manner, the intellectual property
+ notices attached to the Software;
+ .
+ 2. to reproduce said notices, in an identical manner, in the copies
+ of the Software modified or not.
+ .
+ The Licensee undertakes not to directly or indirectly infringe the
+ intellectual property rights of the Holder and/or Contributors on the
+ Software and to take, where applicable, vis-à-vis its staff, any and all
+ measures required to ensure respect of said intellectual property rights
+ of the Holder and/or Contributors.
+ .
+ Article 7 - RELATED SERVICES
+ .
+ 7.1 Under no circumstances shall the Agreement oblige the Licensor to
+ provide technical assistance or maintenance services for the Software.
+ .
+ However, the Licensor is entitled to offer this type of services. The
+ terms and conditions of such technical assistance, and/or such
+ maintenance, shall be set forth in a separate instrument. Only the
+ Licensor offering said maintenance and/or technical assistance services
+ shall incur liability therefor.
+ .
+ 7.2 Similarly, any Licensor is entitled to offer to its licensees, under
+ its sole responsibility, a warranty, that shall only be binding upon
+ itself, for the redistribution of the Software and/or the Modified
+ Software, under terms and conditions that it is free to decide. Said
+ warranty, and the financial terms and conditions of its application,
+ shall be subject of a separate instrument executed between the Licensor
+ and the Licensee.
+ .
+ Article 8 - LIABILITY
+ .
+ 8.1 Subject to the provisions of Article 8.2, the Licensee shall be
+ entitled to claim compensation for any direct loss it may have suffered
+ from the Software as a result of a fault on the part of the relevant
+ Licensor, subject to providing evidence thereof.
+ .
+ 8.2 The Licensor's liability is limited to the commitments made under
+ this Agreement and shall not be incurred as a result of in particular:
+ (i) loss due the Licensee's total or partial failure to fulfill its
+ obligations, (ii) direct or consequential loss that is suffered by the
+ Licensee due to the use or performance of the Software, and (iii) more
+ generally, any consequential loss. In particular the Parties expressly
+ agree that any or all pecuniary or business loss (i.e. loss of data,
+ loss of profits, operating loss, loss of customers or orders,
+ opportunity cost, any disturbance to business activities) or any or all
+ legal proceedings instituted against the Licensee by a third party,
+ shall constitute consequential loss and shall not provide entitlement to
+ any or all compensation from the Licensor.
+ .
+ Article 9 - WARRANTY
+ .
+ 9.1 The Licensee acknowledges that the scientific and technical
+ state-of-the-art when the Software was distributed did not enable all
+ possible uses to be tested and verified, nor for the presence of
+ possible defects to be detected. In this respect, the Licensee's
+ attention has been drawn to the risks associated with loading, using,
+ modifying and/or developing and reproducing the Software which are
+ reserved for experienced users.
+ .
+ The Licensee shall be responsible for verifying, by any or all means,
+ the suitability of the product for its requirements, its good working
+ order, and for ensuring that it shall not cause damage to either persons
+ or properties.
+ .
+ 9.2 The Licensor hereby represents, in good faith, that it is entitled
+ to grant all the rights over the Software (including in particular the
+ rights set forth in Article 5).
+ .
+ 9.3 The Licensee acknowledges that the Software is supplied "as is" by
+ the Licensor without any other express or tacit warranty, other than
+ that provided for in Article 9.2 and, in particular, without any warranty
+ as to its commercial value, its secured, safe, innovative or relevant
+ nature.
+ .
+ Specifically, the Licensor does not warrant that the Software is free
+ from any error, that it will operate without interruption, that it will
+ be compatible with the Licensee's own equipment and software
+ configuration, nor that it will meet the Licensee's requirements.
+ .
+ 9.4 The Licensor does not either expressly or tacitly warrant that the
+ Software does not infringe any third party intellectual property right
+ relating to a patent, software or any other property right. Therefore,
+ the Licensor disclaims any and all liability towards the Licensee
+ arising out of any or all proceedings for infringement that may be
+ instituted in respect of the use, modification and redistribution of the
+ Software. Nevertheless, should such proceedings be instituted against
+ the Licensee, the Licensor shall provide it with technical and legal
+ assistance for its defense. Such technical and legal assistance shall be
+ decided on a case-by-case basis between the relevant Licensor and the
+ Licensee pursuant to a memorandum of understanding. The Licensor
+ disclaims any and all liability as regards the Licensee's use of the
+ name of the Software. No warranty is given as regards the existence of
+ prior rights over the name of the Software or as regards the existence
+ of a trademark.
+ .
+ Article 10 - TERMINATION
+ .
+ 10.1 In the event of a breach by the Licensee of its obligations
+ hereunder, the Licensor may automatically terminate this Agreement
+ thirty (30) days after notice has been sent to the Licensee and has
+ remained ineffective.
+ .
+ 10.2 A Licensee whose Agreement is terminated shall no longer be
+ authorized to use, modify or distribute the Software. However, any
+ licenses that it may have granted prior to termination of the Agreement
+ shall remain valid subject to their having been granted in compliance
+ with the terms and conditions hereof.
+ .
+ Article 11 - MISCELLANEOUS
+ .
+ 11.1 EXCUSABLE EVENTS
+ .
+ Neither Party shall be liable for any or all delay, or failure to
+ perform the Agreement, that may be attributable to an event of force
+ majeure, an act of God or an outside cause, such as defective
+ functioning or interruptions of the electricity or telecommunications
+ networks, network paralysis following a virus attack, intervention by
+ government authorities, natural disasters, water damage, earthquakes,
+ fire, explosions, strikes and labor unrest, war, etc.
+ .
+ 11.2 Any failure by either Party, on one or more occasions, to invoke
+ one or more of the provisions hereof, shall under no circumstances be
+ interpreted as being a waiver by the interested Party of its right to
+ invoke said provision(s) subsequently.
+ .
+ 11.3 The Agreement cancels and replaces any or all previous agreements,
+ whether written or oral, between the Parties and having the same
+ purpose, and constitutes the entirety of the agreement between said
+ Parties concerning said purpose. No supplement or modification to the
+ terms and conditions hereof shall be effective as between the Parties
+ unless it is made in writing and signed by their duly authorized
+ representatives.
+ .
+ 11.4 In the event that one or more of the provisions hereof were to
+ conflict with a current or future applicable act or legislative text,
+ said act or legislative text shall prevail, and the Parties shall make
+ the necessary amendments so as to comply with said act or legislative
+ text. All other provisions shall remain effective. Similarly, invalidity
+ of a provision of the Agreement, for any reason whatsoever, shall not
+ cause the Agreement as a whole to be invalid.
+ .
+ 11.5 LANGUAGE
+ .
+ The Agreement is drafted in both French and English and both versions
+ are deemed authentic.
+ .
+ Article 12 - NEW VERSIONS OF THE AGREEMENT
+ .
+ 12.1 Any person is authorized to duplicate and distribute copies of this
+ Agreement.
+ .
+ 12.2 So as to ensure coherence, the wording of this Agreement is
+ protected and may only be modified by the authors of the License, who
+ reserve the right to periodically publish updates or new versions of the
+ Agreement, each with a separate number. These subsequent versions may
+ address new issues encountered by Free Software.
+ .
+ 12.3 Any Software distributed under a given version of the Agreement may
+ only be subsequently distributed under the same version of the Agreement
+ or a subsequent version, subject to the provisions of Article 5.3.4.
+ .
+ Article 13 - GOVERNING LAW AND JURISDICTION
+ .
+ 13.1 The Agreement is governed by French law. The Parties agree to
+ endeavor to seek an amicable solution to any disagreements or disputes
+ that may arise during the performance of the Agreement.
+ .
+ 13.2 Failing an amicable solution within two (2) months as from their
+ occurrence, and unless emergency proceedings are necessary, the
+ disagreements or disputes shall be referred to the Paris Courts having
+ jurisdiction, by the more diligent Party.
+ .
+ Version 2.0 dated 2006-09-05.
+
+Files: usr/share/biomaj-watcher/src/war/images/appointment-new.png usr/share/biomaj-watcher/src/war/images/bookmark_add.png usr/share/biomaj-watcher/src/war/images/document-properties.png usr/share/biomaj-watcher/src/war/images/document-properties_Disabled.png usr/share/biomaj-watcher/src/war/images/edit-delete.png usr/share/biomaj-watcher/src/war/images/edit-delete_Disabled.png usr/share/biomaj-watcher/src/war/images/normal-update.png usr/share/biomaj-watcher/src/war/images/rebuild-bank [...]
+Copyright: 2006-2007 Everaldo Coelho
+License: LGPL-2.1
+ On Debian systems, the full text of the license
+ can be found in the file
+ `/usr/share/common-licenses/LGPL-2.1'
+
+Files: usr/share/biomaj-watcher/src/war/images/arrow-refresh.png usr/share/biomaj-watcher/src/war/images/clock-go.png usr/share/biomaj-watcher/src/war/images/clock-go_Disabled.png usr/share/biomaj-watcher/src/war/images/group-add.png usr/share/biomaj-watcher/src/war/images/group-go.png usr/share/biomaj-watcher/src/war/images/lock-edit.png usr/share/biomaj-watcher/src/war/images/private.png usr/share/biomaj-watcher/src/war/images/public.png usr/share/biomaj-watcher/src/war/images/page-edi [...]
+Copyright: 2006 Mark James <mjames at gmail.com>
+License: CC-BY-3.0
+ THE WORK (AS DEFINED BELOW) IS PROVIDED UNDER THE TERMS OF THIS CREATIVE COMMONS PUBLIC LICENSE ("CCPL" OR "LICENSE"). THE WORK IS PROTECTED BY COPYRIGHT AND/OR OTHER APPLICABLE LAW. ANY USE OF THE WORK OTHER THAN AS AUTHORIZED UNDER THIS LICENSE OR COPYRIGHT LAW IS PROHIBITED.
+ .
+ BY EXERCISING ANY RIGHTS TO THE WORK PROVIDED HERE, YOU ACCEPT AND AGREE TO BE BOUND BY THE TERMS OF THIS LICENSE. TO THE EXTENT THIS LICENSE MAY BE CONSIDERED TO BE A CONTRACT, THE LICENSOR GRANTS YOU THE RIGHTS CONTAINED HERE IN CONSIDERATION OF YOUR ACCEPTANCE OF SUCH TERMS AND CONDITIONS.
+ .
+ 1. Definitions
+ .
+ "Adaptation" means a work based upon the Work, or upon the Work and other pre-existing works, such as a translation, adaptation, derivative work, arrangement of music or other alterations of a literary or artistic work, or phonogram or performance and includes cinematographic adaptations or any other form in which the Work may be recast, transformed, or adapted including in any form recognizably derived from the original, except that a work that constitutes a Collection will not be cons [...]
+ "Collection" means a collection of literary or artistic works, such as encyclopedias and anthologies, or performances, phonograms or broadcasts, or other works or subject matter other than works listed in Section 1(f) below, which, by reason of the selection and arrangement of their contents, constitute intellectual creations, in which the Work is included in its entirety in unmodified form along with one or more other contributions, each constituting separate and independent works in t [...]
+ "Distribute" means to make available to the public the original and copies of the Work or Adaptation, as appropriate, through sale or other transfer of ownership.
+ "Licensor" means the individual, individuals, entity or entities that offer(s) the Work under the terms of this License.
+ "Original Author" means, in the case of a literary or artistic work, the individual, individuals, entity or entities who created the Work or if no individual or entity can be identified, the publisher; and in addition (i) in the case of a performance the actors, singers, musicians, dancers, and other persons who act, sing, deliver, declaim, play in, interpret or otherwise perform literary or artistic works or expressions of folklore; (ii) in the case of a phonogram the producer being th [...]
+ "Work" means the literary and/or artistic work offered under the terms of this License including without limitation any production in the literary, scientific and artistic domain, whatever may be the mode or form of its expression including digital form, such as a book, pamphlet and other writing; a lecture, address, sermon or other work of the same nature; a dramatic or dramatico-musical work; a choreographic work or entertainment in dumb show; a musical composition with or without wor [...]
+ "You" means an individual or entity exercising rights under this License who has not previously violated the terms of this License with respect to the Work, or who has received express permission from the Licensor to exercise rights under this License despite a previous violation.
+ "Publicly Perform" means to perform public recitations of the Work and to communicate to the public those public recitations, by any means or process, including by wire or wireless means or public digital performances; to make available to the public Works in such a way that members of the public may access these Works from a place and at a place individually chosen by them; to perform the Work to the public by any means or process and the communication to the public of the performances [...]
+ "Reproduce" means to make copies of the Work by any means including without limitation by sound or visual recordings and the right of fixation and reproducing fixations of the Work, including storage of a protected performance or phonogram in digital form or other electronic medium.
+ 2. Fair Dealing Rights. Nothing in this License is intended to reduce, limit, or restrict any uses free from copyright or rights arising from limitations or exceptions that are provided for in connection with the copyright protection under copyright law or other applicable laws.
+ .
+ 3. License Grant. Subject to the terms and conditions of this License, Licensor hereby grants You a worldwide, royalty-free, non-exclusive, perpetual (for the duration of the applicable copyright) license to exercise the rights in the Work as stated below:
+ .
+ to Reproduce the Work, to incorporate the Work into one or more Collections, and to Reproduce the Work as incorporated in the Collections;
+ to create and Reproduce Adaptations provided that any such Adaptation, including any translation in any medium, takes reasonable steps to clearly label, demarcate or otherwise identify that changes were made to the original Work. For example, a translation could be marked "The original work was translated from English to Spanish," or a modification could indicate "The original work has been modified.";
+ to Distribute and Publicly Perform the Work including as incorporated in Collections; and,
+ to Distribute and Publicly Perform Adaptations.
+ For the avoidance of doubt:
+ .
+ Non-waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing scheme cannot be waived, the Licensor reserves the exclusive right to collect such royalties for any exercise by You of the rights granted under this License;
+ Waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing scheme can be waived, the Licensor waives the exclusive right to collect such royalties for any exercise by You of the rights granted under this License; and,
+ Voluntary License Schemes. The Licensor waives the right to collect royalties, whether individually or, in the event that the Licensor is a member of a collecting society that administers voluntary licensing schemes, via that society, from any exercise by You of the rights granted under this License.
+ The above rights may be exercised in all media and formats whether now known or hereafter devised. The above rights include the right to make such modifications as are technically necessary to exercise the rights in other media and formats. Subject to Section 8(f), all rights not expressly granted by Licensor are hereby reserved.
+ .
+ 4. Restrictions. The license granted in Section 3 above is expressly made subject to and limited by the following restrictions:
+ .
+ You may Distribute or Publicly Perform the Work only under the terms of this License. You must include a copy of, or the Uniform Resource Identifier (URI) for, this License with every copy of the Work You Distribute or Publicly Perform. You may not offer or impose any terms on the Work that restrict the terms of this License or the ability of the recipient of the Work to exercise the rights granted to that recipient under the terms of the License. You may not sublicense the Work. You mu [...]
+ If You Distribute, or Publicly Perform the Work or any Adaptations or Collections, You must, unless a request has been made pursuant to Section 4(a), keep intact all copyright notices for the Work and provide, reasonable to the medium or means You are utilizing: (i) the name of the Original Author (or pseudonym, if applicable) if supplied, and/or if the Original Author and/or Licensor designate another party or parties (e.g., a sponsor institute, publishing entity, journal) for attribut [...]
+ Except as otherwise agreed in writing by the Licensor or as may be otherwise permitted by applicable law, if You Reproduce, Distribute or Publicly Perform the Work either by itself or as part of any Adaptations or Collections, You must not distort, mutilate, modify or take other derogatory action in relation to the Work which would be prejudicial to the Original Author's honor or reputation. Licensor agrees that in those jurisdictions (e.g. Japan), in which any exercise of the right gra [...]
+ 5. Representations, Warranties and Disclaimer
+ .
+ UNLESS OTHERWISE MUTUALLY AGREED TO BY THE PARTIES IN WRITING, LICENSOR OFFERS THE WORK AS-IS AND MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE WORK, EXPRESS, IMPLIED, STATUTORY OR OTHERWISE, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF TITLE, MERCHANTIBILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, ACCURACY, OR THE PRESENCE OF ABSENCE OF ERRORS, WHETHER OR NOT DISCOVERABLE. SOME JURISDICTIONS DO NOT ALLOW THE EXC [...]
+ .
+ 6. Limitation on Liability. EXCEPT TO THE EXTENT REQUIRED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE TO YOU ON ANY LEGAL THEORY FOR ANY SPECIAL, INCIDENTAL, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES ARISING OUT OF THIS LICENSE OR THE USE OF THE WORK, EVEN IF LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+ .
+ 7. Termination
+ .
+ This License and the rights granted hereunder will terminate automatically upon any breach by You of the terms of this License. Individuals or entities who have received Adaptations or Collections from You under this License, however, will not have their licenses terminated provided such individuals or entities remain in full compliance with those licenses. Sections 1, 2, 5, 6, 7, and 8 will survive any termination of this License.
+ Subject to the above terms and conditions, the license granted here is perpetual (for the duration of the applicable copyright in the Work). Notwithstanding the above, Licensor reserves the right to release the Work under different license terms or to stop distributing the Work at any time; provided, however that any such election will not serve to withdraw this License (or any other license that has been, or is required to be, granted under the terms of this License), and this License [...]
+ 8. Miscellaneous
+ .
+ Each time You Distribute or Publicly Perform the Work or a Collection, the Licensor offers to the recipient a license to the Work on the same terms and conditions as the license granted to You under this License.
+ Each time You Distribute or Publicly Perform an Adaptation, Licensor offers to the recipient a license to the original Work on the same terms and conditions as the license granted to You under this License.
+ 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 [...]
+
+Files: usr/share/biomaj-watcher/src/war/images/stop.png
+Copyright: Tango harm-on-icons
+License: CC-BY 3.0
+ THE WORK (AS DEFINED BELOW) IS PROVIDED UNDER THE TERMS OF THIS CREATIVE COMMONS PUBLIC LICENSE ("CCPL" OR "LICENSE"). THE WORK IS PROTECTED BY COPYRIGHT AND/OR OTHER APPLICABLE LAW. ANY USE OF THE WORK OTHER THAN AS AUTHORIZED UNDER THIS LICENSE OR COPYRIGHT LAW IS PROHIBITED.
+ .
+ BY EXERCISING ANY RIGHTS TO THE WORK PROVIDED HERE, YOU ACCEPT AND AGREE TO BE BOUND BY THE TERMS OF THIS LICENSE. TO THE EXTENT THIS LICENSE MAY BE CONSIDERED TO BE A CONTRACT, THE LICENSOR GRANTS YOU THE RIGHTS CONTAINED HERE IN CONSIDERATION OF YOUR ACCEPTANCE OF SUCH TERMS AND CONDITIONS.
+ .
+ 1. Definitions
+ .
+ "Adaptation" means a work based upon the Work, or upon the Work and other pre-existing works, such as a translation, adaptation, derivative work, arrangement of music or other alterations of a literary or artistic work, or phonogram or performance and includes cinematographic adaptations or any other form in which the Work may be recast, transformed, or adapted including in any form recognizably derived from the original, except that a work that constitutes a Collection will not be cons [...]
+ "Collection" means a collection of literary or artistic works, such as encyclopedias and anthologies, or performances, phonograms or broadcasts, or other works or subject matter other than works listed in Section 1(f) below, which, by reason of the selection and arrangement of their contents, constitute intellectual creations, in which the Work is included in its entirety in unmodified form along with one or more other contributions, each constituting separate and independent works in t [...]
+ "Distribute" means to make available to the public the original and copies of the Work or Adaptation, as appropriate, through sale or other transfer of ownership.
+ "Licensor" means the individual, individuals, entity or entities that offer(s) the Work under the terms of this License.
+ "Original Author" means, in the case of a literary or artistic work, the individual, individuals, entity or entities who created the Work or if no individual or entity can be identified, the publisher; and in addition (i) in the case of a performance the actors, singers, musicians, dancers, and other persons who act, sing, deliver, declaim, play in, interpret or otherwise perform literary or artistic works or expressions of folklore; (ii) in the case of a phonogram the producer being th [...]
+ "Work" means the literary and/or artistic work offered under the terms of this License including without limitation any production in the literary, scientific and artistic domain, whatever may be the mode or form of its expression including digital form, such as a book, pamphlet and other writing; a lecture, address, sermon or other work of the same nature; a dramatic or dramatico-musical work; a choreographic work or entertainment in dumb show; a musical composition with or without wor [...]
+ "You" means an individual or entity exercising rights under this License who has not previously violated the terms of this License with respect to the Work, or who has received express permission from the Licensor to exercise rights under this License despite a previous violation.
+ "Publicly Perform" means to perform public recitations of the Work and to communicate to the public those public recitations, by any means or process, including by wire or wireless means or public digital performances; to make available to the public Works in such a way that members of the public may access these Works from a place and at a place individually chosen by them; to perform the Work to the public by any means or process and the communication to the public of the performances [...]
+ "Reproduce" means to make copies of the Work by any means including without limitation by sound or visual recordings and the right of fixation and reproducing fixations of the Work, including storage of a protected performance or phonogram in digital form or other electronic medium.
+ 2. Fair Dealing Rights. Nothing in this License is intended to reduce, limit, or restrict any uses free from copyright or rights arising from limitations or exceptions that are provided for in connection with the copyright protection under copyright law or other applicable laws.
+ .
+ 3. License Grant. Subject to the terms and conditions of this License, Licensor hereby grants You a worldwide, royalty-free, non-exclusive, perpetual (for the duration of the applicable copyright) license to exercise the rights in the Work as stated below:
+ .
+ to Reproduce the Work, to incorporate the Work into one or more Collections, and to Reproduce the Work as incorporated in the Collections;
+ to create and Reproduce Adaptations provided that any such Adaptation, including any translation in any medium, takes reasonable steps to clearly label, demarcate or otherwise identify that changes were made to the original Work. For example, a translation could be marked "The original work was translated from English to Spanish," or a modification could indicate "The original work has been modified.";
+ to Distribute and Publicly Perform the Work including as incorporated in Collections; and,
+ to Distribute and Publicly Perform Adaptations.
+ For the avoidance of doubt:
+ .
+ Non-waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing scheme cannot be waived, the Licensor reserves the exclusive right to collect such royalties for any exercise by You of the rights granted under this License;
+ Waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing scheme can be waived, the Licensor waives the exclusive right to collect such royalties for any exercise by You of the rights granted under this License; and,
+ Voluntary License Schemes. The Licensor waives the right to collect royalties, whether individually or, in the event that the Licensor is a member of a collecting society that administers voluntary licensing schemes, via that society, from any exercise by You of the rights granted under this License.
+ The above rights may be exercised in all media and formats whether now known or hereafter devised. The above rights include the right to make such modifications as are technically necessary to exercise the rights in other media and formats. Subject to Section 8(f), all rights not expressly granted by Licensor are hereby reserved.
+ .
+ 4. Restrictions. The license granted in Section 3 above is expressly made subject to and limited by the following restrictions:
+ .
+ You may Distribute or Publicly Perform the Work only under the terms of this License. You must include a copy of, or the Uniform Resource Identifier (URI) for, this License with every copy of the Work You Distribute or Publicly Perform. You may not offer or impose any terms on the Work that restrict the terms of this License or the ability of the recipient of the Work to exercise the rights granted to that recipient under the terms of the License. You may not sublicense the Work. You mu [...]
+ If You Distribute, or Publicly Perform the Work or any Adaptations or Collections, You must, unless a request has been made pursuant to Section 4(a), keep intact all copyright notices for the Work and provide, reasonable to the medium or means You are utilizing: (i) the name of the Original Author (or pseudonym, if applicable) if supplied, and/or if the Original Author and/or Licensor designate another party or parties (e.g., a sponsor institute, publishing entity, journal) for attribut [...]
+ Except as otherwise agreed in writing by the Licensor or as may be otherwise permitted by applicable law, if You Reproduce, Distribute or Publicly Perform the Work either by itself or as part of any Adaptations or Collections, You must not distort, mutilate, modify or take other derogatory action in relation to the Work which would be prejudicial to the Original Author's honor or reputation. Licensor agrees that in those jurisdictions (e.g. Japan), in which any exercise of the right gra [...]
+ 5. Representations, Warranties and Disclaimer
+ .
+ UNLESS OTHERWISE MUTUALLY AGREED TO BY THE PARTIES IN WRITING, LICENSOR OFFERS THE WORK AS-IS AND MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE WORK, EXPRESS, IMPLIED, STATUTORY OR OTHERWISE, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF TITLE, MERCHANTIBILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, ACCURACY, OR THE PRESENCE OF ABSENCE OF ERRORS, WHETHER OR NOT DISCOVERABLE. SOME JURISDICTIONS DO NOT ALLOW THE EXC [...]
+ .
+ 6. Limitation on Liability. EXCEPT TO THE EXTENT REQUIRED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE TO YOU ON ANY LEGAL THEORY FOR ANY SPECIAL, INCIDENTAL, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES ARISING OUT OF THIS LICENSE OR THE USE OF THE WORK, EVEN IF LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+ .
+ 7. Termination
+ .
+ This License and the rights granted hereunder will terminate automatically upon any breach by You of the terms of this License. Individuals or entities who have received Adaptations or Collections from You under this License, however, will not have their licenses terminated provided such individuals or entities remain in full compliance with those licenses. Sections 1, 2, 5, 6, 7, and 8 will survive any termination of this License.
+ Subject to the above terms and conditions, the license granted here is perpetual (for the duration of the applicable copyright in the Work). Notwithstanding the above, Licensor reserves the right to release the Work under different license terms or to stop distributing the Work at any time; provided, however that any such election will not serve to withdraw this License (or any other license that has been, or is required to be, granted under the terms of this License), and this License [...]
+ 8. Miscellaneous
+ .
+ Each time You Distribute or Publicly Perform the Work or a Collection, the Licensor offers to the recipient a license to the Work on the same terms and conditions as the license granted to You under this License.
+ Each time You Distribute or Publicly Perform an Adaptation, Licensor offers to the recipient a license to the original Work on the same terms and conditions as the license granted to You under this License.
+ 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 [...]
+
+Files: usr/share/biomaj-watcher/src/war/images/bank-detail.png usr/share/biomaj-watcher/src/war/images/bank-detail_Disabled.png usr/share/biomaj-watcher/src/war/images/code-block.png usr/share/biomaj-watcher/src/war/images/help-hint.png usr/share/biomaj-watcher/src/war/images/vcs-conflicting.png usr/share/biomaj-watcher/src/war/images/view-calendar.png
+Copyright: 2007-2009, David Vignoni <david at icon-king.com>
+ 2007-2009, Johann Ollivier Lapeyre <johann at oxygen-icons.org>
+ 2007-2009, Kenneth Wimer <kwwii at bootsplash.org>
+ 2007-2009, Nuno Fernades Pinheiro <nf.pinheiro at gmail.com>
+ 2007-2009, Riccardo Iaconelli <riccardo at oxygen-icons.org>
+ 2007-2009, David Miller <miller at oxygen-icons.org>
+License: LGPL-2.1
+ On Debian systems, the full text of the license
+ can be found in the file
+ `/usr/share/common-licenses/LGPL-2.1'
+
+
+Files: usr/share/biomaj-watcher/src/war/images/edit-find-5.png usr/share/biomaj-watcher/src/war/images/update_all.png usr/share/biomaj-watcher/src/war/images/update_all_Disabled.pngusr/share/biomaj-watcher/src/war/images/view-refresh.png usr/share/biomaj-watcher/src/war/images/zoom-3.png
+Copyright: 2003-2004 David Vignoni
+License: LGPL-2.1
+ On Debian systems, the full text of the license
+ can be found in the file
+ `/usr/share/common-licenses/LGPL-2.1'
+
+Files: usr/share/biomaj-watcher/src/war/images/edit-redo.png usr/share/biomaj-watcher/src/war/images/help-hint.png usr/share/biomaj-watcher/src/war/images/list-remove.png
+Copyright: Intrigue Icon Set 0.6.2 [Green]
+License: GPL-2
+ On Debian systems, the full text of the license
+ can be found in the file
+ `/usr/share/common-licenses/GPL-2'
+
+Files: usr/share/biomaj-watcher/src/war/images/help-about.png
+Copyright: GNOME Icon Theme 2.26.0 (gnome)
+License: GPL-2
+ On Debian systems, the full text of the license
+ can be found in the file
+ `/usr/share/common-licenses/GPL-2'
+
+Files: usr/share/biomaj-watcher/src/war/images/view-refresh-4.png
+Copyright: Tango Icon Library 0.8.90
+License: GPL-2
+ On Debian systems, the full text of the license
+ can be found in the file
+ `/usr/share/common-licenses/GPL-2'
+
+
+Files: usr/share/biomaj-watcher/src/extlib/smartgwt.jar usr/share/biomaj-watcher/src/extlib/smartgwt-skins.jar
+Copyright: 2008 and beyond Isomorphic software
+License: LGPL-3
+ On Debian systems, the full text of the license
+ can be found in the file
+ `/usr/share/common-licenses/LGPL-3'
+
+Files: usr/share/biomaj-watcher/src/extlib/gwt-visualization.jar
+Copyright: 2010 Google
+License: Apache 2.0
+ On Debian systems, the full text of the license
+ can be found in the file
+ `/usr/share/common-licenses/Apache-2.0'
+
+
+Files: usr/share/biomaj-watcher/src/extlib/gwt-dnd-3.0.1.jar usr/share/biomaj-watcher/src/extlib/gwt-cal-0.9.0.jar
+Copyright: 2009,2010 Scottsdale Software LCC
+License: GPL v3+
+ On Debian systems, the full text of the GNU General Public
+ License version 3 can be found in the file
+ `/usr/share/common-licenses/GPL-3'
+
+
+Files: usr/share/biomaj-watcher/src/gwt/*
+Copyright:
+ Copyright 2010 Google
+ Includes Apache Tomcat Copyright Apache Foundation, license Apache 2.0
+ Includes Browser Detect v2.1.6 Copyright XXX, license Creative Commons Attribution 1.0
+ Includes Eclipse Java Development Tools Copyright XXX, license Eclipse Public License v. 1.0
+ Includes Eclipse Standard Widget Toolkit Copyright XXX, license Eclipse Public License v. 1.0
+ Includes HtmlUnit Copyright XXX, license Apache 2.0
+ Includes JFreeChart Copyright XXX, license LGPL v2.1
+ Includes Mozilla Rhino Copyright XXX, license Mozilla Public License v. 1.1
+ Includes Mozilla 1.7.12 Copyright XXX, license Mozilla Public License V. 1.1
+ Includes Protocol Buffers Copyright XXX, license BSD 2
+License:
+ Includes Browser Detect licensed under terms:
+ THE WORK (AS DEFINED BELOW) IS PROVIDED UNDER THE TERMS OF THIS CREATIVE COMMONS PUBLIC LICENSE ("CCPL" OR "LICENSE"). THE WORK IS PROTECTED BY COPYRIGHT AND/OR OTHER APPLICABLE LAW. ANY USE OF THE WORK OTHER THAN AS AUTHORIZED UNDER THIS LICENSE OR COPYRIGHT LAW IS PROHIBITED.
+ .
+ BY EXERCISING ANY RIGHTS TO THE WORK PROVIDED HERE, YOU ACCEPT AND AGREE TO BE BOUND BY THE TERMS OF THIS LICENSE. TO THE EXTENT THIS LICENSE MAY BE CONSIDERED TO BE A CONTRACT, THE LICENSOR GRANTS YOU THE RIGHTS CONTAINED HERE IN CONSIDERATION OF YOUR ACCEPTANCE OF SUCH TERMS AND CONDITIONS.
+ .
+ 1. Definitions
+ .
+ "Collective Work" means a work, such as a periodical issue, anthology or encyclopedia, in which the Work in its entirety in unmodified form, along with one or more other contributions, constituting separate and independent works in themselves, are assembled into a collective whole. A work that constitutes a Collective Work will not be considered a Derivative Work (as defined below) for the purposes of this License.
+ "Derivative Work" means a work based upon the Work or upon the Work and other pre-existing works, such as a translation, musical arrangement, dramatization, fictionalization, motion picture version, sound recording, art reproduction, abridgment, condensation, or any other form in which the Work may be recast, transformed, or adapted, except that a work that constitutes a Collective Work will not be considered a Derivative Work for the purpose of this License. For the avoidance of doubt, [...]
+ "Licensor" means the individual, individuals, entity or entities that offers the Work under the terms of this License.
+ "Original Author" means the individual, individuals, entity or entities who created the Work.
+ "Work" means the copyrightable work of authorship offered under the terms of this License.
+ "You" means an individual or entity exercising rights under this License who has not previously violated the terms of this License with respect to the Work, or who has received express permission from the Licensor to exercise rights under this License despite a previous violation.
+ 2. Fair Use Rights. Nothing in this license is intended to reduce, limit, or restrict any rights arising from fair use, first sale or other limitations on the exclusive rights of the copyright owner under copyright law or other applicable laws.
+ .
+ 3. License Grant. Subject to the terms and conditions of this License, Licensor hereby grants You a worldwide, royalty-free, non-exclusive, perpetual (for the duration of the applicable copyright) license to exercise the rights in the Work as stated below:
+ .
+ to reproduce the Work, to incorporate the Work into one or more Collective Works, and to reproduce the Work as incorporated in the Collective Works;
+ to create and reproduce Derivative Works provided that any such Derivative Work, including any translation in any medium, takes reasonable steps to clearly label, demarcate or otherwise identify that changes were made to the original Work. For example, a translation could be marked "The original work was translated from English to Spanish," or a modification could indicate "The original work has been modified.";;
+ to distribute copies or phonorecords of, display publicly, perform publicly, and perform publicly by means of a digital audio transmission the Work including as incorporated in Collective Works;
+ to distribute copies or phonorecords of, display publicly, perform publicly, and perform publicly by means of a digital audio transmission Derivative Works.
+ For the avoidance of doubt, where the Work is a musical composition:
+ .
+ Performance Royalties Under Blanket Licenses. Licensor waives the exclusive right to collect, whether individually or, in the event that Licensor is a member of a performance rights society (e.g. ASCAP, BMI, SESAC), via that society, royalties for the public performance or public digital performance (e.g. webcast) of the Work.
+ Mechanical Rights and Statutory Royalties. Licensor waives the exclusive right to collect, whether individually or via a music rights agency or designated agent (e.g. Harry Fox Agency), royalties for any phonorecord You create from the Work ("cover version") and distribute, subject to the compulsory license created by 17 USC Section 115 of the US Copyright Act (or the equivalent in other jurisdictions).
+ Webcasting Rights and Statutory Royalties. For the avoidance of doubt, where the Work is a sound recording, Licensor waives the exclusive right to collect, whether individually or via a performance-rights society (e.g. SoundExchange), royalties for the public digital performance (e.g. webcast) of the Work, subject to the compulsory license created by 17 USC Section 114 of the US Copyright Act (or the equivalent in other jurisdictions).
+ The above rights may be exercised in all media and formats whether now known or hereafter devised. The above rights include the right to make such modifications as are technically necessary to exercise the rights in other media and formats. All rights not expressly granted by Licensor are hereby reserved.
+ .
+ 4. Restrictions. The license granted in Section 3 above is expressly made subject to and limited by the following restrictions:
+ .
+ You may distribute, publicly display, publicly perform, or publicly digitally perform the Work only under the terms of this License, and You must include a copy of, or the Uniform Resource Identifier for, this License with every copy or phonorecord of the Work You distribute, publicly display, publicly perform, or publicly digitally perform. You may not offer or impose any terms on the Work that restrict the terms of this License or the ability of a recipient of the Work to exercise the [...]
+ If You distribute, publicly display, publicly perform, or publicly digitally perform the Work (as defined in Section 1 above) or any Derivative Works (as defined in Section 1 above) or Collective Works (as defined in Section 1 above), You must, unless a request has been made pursuant to Section 4(a), keep intact all copyright notices for the Work and provide, reasonable to the medium or means You are utilizing: (i) the name of the Original Author (or pseudonym, if applicable) if supplie [...]
+ 5. Representations, Warranties and Disclaimer
+ .
+ UNLESS OTHERWISE MUTUALLY AGREED TO BY THE PARTIES IN WRITING, LICENSOR OFFERS THE WORK AS-IS AND ONLY TO THE EXTENT OF ANY RIGHTS HELD IN THE LICENSED WORK BY THE LICENSOR. THE LICENSOR MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE WORK, EXPRESS, IMPLIED, STATUTORY OR OTHERWISE, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF TITLE, MARKETABILITY, MERCHANTIBILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, ACCURACY, OR [...]
+ .
+ 6. Limitation on Liability. EXCEPT TO THE EXTENT REQUIRED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE TO YOU ON ANY LEGAL THEORY FOR ANY SPECIAL, INCIDENTAL, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES ARISING OUT OF THIS LICENSE OR THE USE OF THE WORK, EVEN IF LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+ .
+ 7. Termination
+ .
+ This License and the rights granted hereunder will terminate automatically upon any breach by You of the terms of this License. Individuals or entities who have received Derivative Works (as defined in Section 1 above) or Collective Works (as defined in Section 1 above) from You under this License, however, will not have their licenses terminated provided such individuals or entities remain in full compliance with those licenses. Sections 1, 2, 5, 6, 7, and 8 will survive any terminatio [...]
+ Subject to the above terms and conditions, the license granted here is perpetual (for the duration of the applicable copyright in the Work). Notwithstanding the above, Licensor reserves the right to release the Work under different license terms or to stop distributing the Work at any time; provided, however that any such election will not serve to withdraw this License (or any other license that has been, or is required to be, granted under the terms of this License), and this License [...]
+ 8. Miscellaneous
+ .
+ Each time You distribute or publicly digitally perform the Work (as defined in Section 1 above) or a Collective Work (as defined in Section 1 above), the Licensor offers to the recipient a license to the Work on the same terms and conditions as the license granted to You under this License.
+ Each time You distribute or publicly digitally perform a Derivative Work, Licensor offers to the recipient a license to the original Work on the same terms and conditions as the license granted to You under this License.
+ 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.
+ .
+ Includes Eclipse Java Development Tools and Standard Widget Toolkt licensed under terms:
+ THE ACCOMPANYING PROGRAM IS PROVIDED UNDER THE TERMS OF THIS ECLIPSE PUBLIC LICENSE ("AGREEMENT"). ANY USE, REPRODUCTION OR DISTRIBUTION OF THE PROGRAM CONSTITUTES RECIPIENT'S ACCEPTANCE OF THIS AGREEMENT.
+ .
+ 1. DEFINITIONS
+ .
+ "Contribution" means:
+ .
+ a) in the case of the initial Contributor, the initial code and documentation distributed under this Agreement, and
+ b) in the case of each subsequent Contributor:
+ i) changes to the Program, and
+ ii) additions to the Program;
+ where such changes and/or additions to the Program originate from and are distributed by that particular Contributor. A Contribution 'originates' from a Contributor if it was added to the Program by such Contributor itself or anyone acting on such Contributor's behalf. Contributions do not include additions to the Program which: (i) are separate modules of software distributed in conjunction with the Program under their own license agreement, and (ii) are not derivative works of the Program.
+ "Contributor" means any person or entity that distributes the Program.
+ .
+ "Licensed Patents" mean patent claims licensable by a Contributor which are necessarily infringed by the use or sale of its Contribution alone or when combined with the Program.
+ .
+ "Program" means the Contributions distributed in accordance with this Agreement.
+ .
+ "Recipient" means anyone who receives the Program under this Agreement, including all Contributors.
+ .
+ 2. GRANT OF RIGHTS
+ .
+ a) Subject to the terms of this Agreement, each Contributor hereby grants Recipient a non-exclusive, worldwide, royalty-free copyright license to reproduce, prepare derivative works of, publicly display, publicly perform, distribute and sublicense the Contribution of such Contributor, if any, and such derivative works, in source code and object code form.
+ b) Subject to the terms of this Agreement, each Contributor hereby grants Recipient a non-exclusive, worldwide, royalty-free patent license under Licensed Patents to make, use, sell, offer to sell, import and otherwise transfer the Contribution of such Contributor, if any, in source code and object code form. This patent license shall apply to the combination of the Contribution and the Program if, at the time the Contribution is added by the Contributor, such addition of the Contributi [...]
+ c) Recipient understands that although each Contributor grants the licenses to its Contributions set forth herein, no assurances are provided by any Contributor that the Program does not infringe the patent or other intellectual property rights of any other entity. Each Contributor disclaims any liability to Recipient for claims brought by any other entity based on infringement of intellectual property rights or otherwise. As a condition to exercising the rights and licenses granted her [...]
+ d) Each Contributor represents that to its knowledge it has sufficient copyright rights in its Contribution, if any, to grant the copyright license set forth in this Agreement.
+ 3. REQUIREMENTS
+ .
+ A Contributor may choose to distribute the Program in object code form under its own license agreement, provided that:
+ .
+ a) it complies with the terms and conditions of this Agreement; and
+ b) its license agreement:
+ i) effectively disclaims on behalf of all Contributors all warranties and conditions, express and implied, including warranties or conditions of title and non-infringement, and implied warranties or conditions of merchantability and fitness for a particular purpose;
+ ii) effectively excludes on behalf of all Contributors all liability for damages, including direct, indirect, special, incidental and consequential damages, such as lost profits;
+ iii) states that any provisions which differ from this Agreement are offered by that Contributor alone and not by any other party; and
+ iv) states that source code for the Program is available from such Contributor, and informs licensees how to obtain it in a reasonable manner on or through a medium customarily used for software exchange.
+ When the Program is made available in source code form:
+ .
+ a) it must be made available under this Agreement; and
+ b) a copy of this Agreement must be included with each copy of the Program.
+ Contributors may not remove or alter any copyright notices contained within the Program.
+ .
+ Each Contributor must identify itself as the originator of its Contribution, if any, in a manner that reasonably allows subsequent Recipients to identify the originator of the Contribution.
+ .
+ 4. COMMERCIAL DISTRIBUTION
+ .
+ Commercial distributors of software may accept certain responsibilities with respect to end users, business partners and the like. While this license is intended to facilitate the commercial use of the Program, the Contributor who includes the Program in a commercial product offering should do so in a manner which does not create potential liability for other Contributors. Therefore, if a Contributor includes the Program in a commercial product offering, such Contributor ("Commercial Co [...]
+ .
+ For example, a Contributor might include the Program in a commercial product offering, Product X. That Contributor is then a Commercial Contributor. If that Commercial Contributor then makes performance claims, or offers warranties related to Product X, those performance claims and warranties are such Commercial Contributor's responsibility alone. Under this section, the Commercial Contributor would have to defend claims against the other Contributors related to those performance claims [...]
+ .
+ 5. NO WARRANTY
+ .
+ EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, THE PROGRAM IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED INCLUDING, WITHOUT LIMITATION, ANY WARRANTIES OR CONDITIONS OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Each Recipient is solely responsible for determining the appropriateness of using and distributing the Program and assumes all risks associated with its exercise of rights under this A [...]
+ .
+ 6. DISCLAIMER OF LIABILITY
+ .
+ EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, NEITHER RECIPIENT NOR ANY CONTRIBUTORS SHALL HAVE ANY LIABILITY FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING WITHOUT LIMITATION LOST PROFITS), HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OR DISTRIBUTION OF THE PROGRAM OR THE EXERCISE OF ANY RIGHTS GRANTED HEREUNDER, EVEN I [...]
+ .
+ 7. GENERAL
+ .
+ If any provision of this Agreement is invalid or unenforceable under applicable law, it shall not affect the validity or enforceability of the remainder of the terms of this Agreement, and without further action by the parties hereto, such provision shall be reformed to the minimum extent necessary to make such provision valid and enforceable.
+ .
+ If Recipient institutes patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Program itself (excluding combinations of the Program with other software or hardware) infringes such Recipient's patent(s), then such Recipient's rights granted under Section 2(b) shall terminate as of the date such litigation is filed.
+ .
+ All Recipient's rights under this Agreement shall terminate if it fails to comply with any of the material terms or conditions of this Agreement and does not cure such failure in a reasonable period of time after becoming aware of such noncompliance. If all Recipient's rights under this Agreement terminate, Recipient agrees to cease use and distribution of the Program as soon as reasonably practicable. However, Recipient's obligations under this Agreement and any licenses granted by Rec [...]
+ .
+ Everyone is permitted to copy and distribute copies of this Agreement, but in order to avoid inconsistency the Agreement is copyrighted and may only be modified in the following manner. The Agreement Steward reserves the right to publish new versions (including revisions) of this Agreement from time to time. No one other than the Agreement Steward has the right to modify this Agreement. The Eclipse Foundation is the initial Agreement Steward. The Eclipse Foundation may assign the respon [...]
+ .
+ This Agreement is governed by the laws of the State of New York and the intellectual property laws of the United States of America. No party to this Agreement will bring a legal action under this Agreement more than one year after the cause of action arose. Each party waives its rights to a jury trial in any resulting litigation.
+ Includes Mozilla Rhino and Mozilla licensed unter terms:
+ 1. Definitions.
+ .
+ 1.0.1. "Commercial Use"
+ means distribution or otherwise making the Covered Code available to a third party.
+ 1.1. "Contributor"
+ means each entity that creates or contributes to the creation of Modifications.
+ 1.2. "Contributor Version"
+ means the combination of the Original Code, prior Modifications used by a Contributor, and the Modifications made by that particular Contributor.
+ 1.3. "Covered Code"
+ means the Original Code or Modifications or the combination of the Original Code and Modifications, in each case including portions thereof.
+ 1.4. "Electronic Distribution Mechanism"
+ means a mechanism generally accepted in the software development community for the electronic transfer of data.
+ 1.5. "Executable"
+ means Covered Code in any form other than Source Code.
+ 1.6. "Initial Developer"
+ means the individual or entity identified as the Initial Developer in the Source Code notice required by Exhibit A.
+ 1.7. "Larger Work"
+ means a work which combines Covered Code or portions thereof with code not governed by the terms of this License.
+ 1.8. "License"
+ means this document.
+ 1.8.1. "Licensable"
+ means having the right to grant, to the maximum extent possible, whether at the time of the initial grant or subsequently acquired, any and all of the rights conveyed herein.
+ 1.9. "Modifications"
+ means any addition to or deletion from the substance or structure of either the Original Code or any previous Modifications. When Covered Code is released as a series of files, a Modification is:
+ Any addition to or deletion from the contents of a file containing Original Code or previous Modifications.
+ Any new file that contains any part of the Original Code or previous Modifications.
+ 1.10. "Original Code"
+ means Source Code of computer software code which is described in the Source Code notice required by Exhibit A as Original Code, and which, at the time of its release under this License is not already Covered Code governed by this License.
+ 1.10.1. "Patent Claims"
+ means any patent claim(s), now owned or hereafter acquired, including without limitation, method, process, and apparatus claims, in any patent Licensable by grantor.
+ 1.11. "Source Code"
+ means the preferred form of the Covered Code for making modifications to it, including all modules it contains, plus any associated interface definition files, scripts used to control compilation and installation of an Executable, or source code differential comparisons against either the Original Code or another well known, available Covered Code of the Contributor's choice. The Source Code can be in a compressed or archival form, provided the appropriate decompression or de-archiving [...]
+ 1.12. "You" (or "Your")
+ means an individual or a legal entity exercising rights under, and complying with all of the terms of, this License or a future version of this License issued under Section 6.1. For legal entities, "You" includes any entity which controls, is controlled by, or is under common control with You. For purposes of this definition, "control" means (a) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (b) ownership of more [...]
+ 2. Source Code License.
+ .
+ 2.1. The Initial Developer Grant.
+ .
+ The Initial Developer hereby grants You a world-wide, royalty-free, non-exclusive license, subject to third party intellectual property claims:
+ .
+ under intellectual property rights (other than patent or trademark) Licensable by Initial Developer to use, reproduce, modify, display, perform, sublicense and distribute the Original Code (or portions thereof) with or without Modifications, and/or as part of a Larger Work; and
+ under Patents Claims infringed by the making, using or selling of Original Code, to make, have made, use, practice, sell, and offer for sale, and/or otherwise dispose of the Original Code (or portions thereof).
+ the licenses granted in this Section 2.1 (a) and (b) are effective on the date Initial Developer first distributes Original Code under the terms of this License.
+ Notwithstanding Section 2.1 (b) above, no patent license is granted: 1) for code that You delete from the Original Code; 2) separate from the Original Code; or 3) for infringements caused by: i) the modification of the Original Code or ii) the combination of the Original Code with other software or devices.
+ 2.2. Contributor Grant.
+ .
+ Subject to third party intellectual property claims, each Contributor hereby grants You a world-wide, royalty-free, non-exclusive license
+ .
+ under intellectual property rights (other than patent or trademark) Licensable by Contributor, to use, reproduce, modify, display, perform, sublicense and distribute the Modifications created by such Contributor (or portions thereof) either on an unmodified basis, with other Modifications, as Covered Code and/or as part of a Larger Work; and
+ under Patent Claims infringed by the making, using, or selling of Modifications made by that Contributor either alone and/or in combination with its Contributor Version (or portions of such combination), to make, use, sell, offer for sale, have made, and/or otherwise dispose of: 1) Modifications made by that Contributor (or portions thereof); and 2) the combination of Modifications made by that Contributor with its Contributor Version (or portions of such combination).
+ the licenses granted in Sections 2.2 (a) and 2.2 (b) are effective on the date Contributor first makes Commercial Use of the Covered Code.
+ Notwithstanding Section 2.2 (b) above, no patent license is granted: 1) for any code that Contributor has deleted from the Contributor Version; 2) separate from the Contributor Version; 3) for infringements caused by: i) third party modifications of Contributor Version or ii) the combination of Modifications made by that Contributor with other software (except as part of the Contributor Version) or other devices; or 4) under Patent Claims infringed by Covered Code in the absence of Modi [...]
+ 3. Distribution Obligations.
+ .
+ 3.1. Application of License.
+ .
+ The Modifications which You create or to which You contribute are governed by the terms of this License, including without limitation Section 2.2. The Source Code version of Covered Code may be distributed only under the terms of this License or a future version of this License released under Section 6.1, and You must include a copy of this License with every copy of the Source Code You distribute. You may not offer or impose any terms on any Source Code version that alters or restricts [...]
+ .
+ 3.2. Availability of Source Code.
+ .
+ Any Modification which You create or to which You contribute must be made available in Source Code form under the terms of this License either on the same media as an Executable version or via an accepted Electronic Distribution Mechanism to anyone to whom you made an Executable version available; and if made available via Electronic Distribution Mechanism, must remain available for at least twelve (12) months after the date it initially became available, or at least six (6) months afte [...]
+ .
+ 3.3. Description of Modifications.
+ .
+ You must cause all Covered Code to which You contribute to contain a file documenting the changes You made to create that Covered Code and the date of any change. You must include a prominent statement that the Modification is derived, directly or indirectly, from Original Code provided by the Initial Developer and including the name of the Initial Developer in (a) the Source Code, and (b) in any notice in an Executable version or related documentation in which You describe the origin o [...]
+ .
+ 3.4. Intellectual Property Matters
+ .
+ (a) Third Party Claims
+ .
+ If Contributor has knowledge that a license under a third party's intellectual property rights is required to exercise the rights granted by such Contributor under Sections 2.1 or 2.2, Contributor must include a text file with the Source Code distribution titled "LEGAL" which describes the claim and the party making the claim in sufficient detail that a recipient will know whom to contact. If Contributor obtains such knowledge after the Modification is made available as described in Sec [...]
+ .
+ (b) Contributor APIs
+ .
+ If Contributor's Modifications include an application programming interface and Contributor has knowledge of patent licenses which are reasonably necessary to implement that API, Contributor must also include this information in the LEGAL file.
+ .
+ (c) Representations.
+ .
+ Contributor represents that, except as disclosed pursuant to Section 3.4 (a) above, Contributor believes that Contributor's Modifications are Contributor's original creation(s) and/or Contributor has sufficient rights to grant the rights conveyed by this License.
+ .
+ 3.5. Required Notices.
+ .
+ You must duplicate the notice in Exhibit A in each file of the Source Code. If it is not possible to put such notice in a particular Source Code file due to its structure, then You must include such notice in a location (such as a relevant directory) where a user would be likely to look for such a notice. If You created one or more Modification(s) You may add your name as a Contributor to the notice described in Exhibit A. You must also duplicate this License in any documentation for th [...]
+ .
+ 3.6. Distribution of Executable Versions.
+ .
+ You may distribute Covered Code in Executable form only if the requirements of Sections 3.1, 3.2, 3.3, 3.4 and 3.5 have been met for that Covered Code, and if You include a notice stating that the Source Code version of the Covered Code is available under the terms of this License, including a description of how and where You have fulfilled the obligations of Section 3.2. The notice must be conspicuously included in any notice in an Executable version, related documentation or collatera [...]
+ .
+ 3.7. Larger Works.
+ .
+ You may create a Larger Work by combining Covered Code with other code not governed by the terms of this License and distribute the Larger Work as a single product. In such a case, You must make sure the requirements of this License are fulfilled for the Covered Code.
+ .
+ 4. Inability to Comply Due to Statute or Regulation.
+ .
+ If it is impossible for You to comply with any of the terms of this License with respect to some or all of the Covered Code due to statute, judicial order, or regulation then You must: (a) comply with the terms of this License to the maximum extent possible; and (b) describe the limitations and the code they affect. Such description must be included in the LEGAL file described in Section 3.4 and must be included with all distributions of the Source Code. Except to the extent prohibited [...]
+ .
+ 5. Application of this License.
+ .
+ This License applies to code to which the Initial Developer has attached the notice in Exhibit A and to related Covered Code.
+ .
+ 6. Versions of the License.
+ .
+ 6.1. New Versions
+ .
+ Netscape Communications Corporation ("Netscape") may publish revised and/or new versions of the License from time to time. Each version will be given a distinguishing version number.
+ .
+ 6.2. Effect of New Versions
+ .
+ Once Covered Code has been published under a particular version of the License, You may always continue to use it under the terms of that version. You may also choose to use such Covered Code under the terms of any subsequent version of the License published by Netscape. No one other than Netscape has the right to modify the terms applicable to Covered Code created under this License.
+ .
+ 6.3. Derivative Works
+ .
+ If You create or use a modified version of this License (which you may only do in order to apply it to code which is not already Covered Code governed by this License), You must (a) rename Your license so that the phrases "Mozilla", "MOZILLAPL", "MOZPL", "Netscape", "MPL", "NPL" or any confusingly similar phrase do not appear in your license (except to note that your license differs from this License) and (b) otherwise make it clear that Your version of the license contains terms which [...]
+ .
+ 7. DISCLAIMER OF WARRANTY
+ .
+ COVERED CODE IS PROVIDED UNDER THIS LICENSE ON AN "AS IS" BASIS, WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES THAT THE COVERED CODE IS FREE OF DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE COVERED CODE IS WITH YOU. SHOULD ANY COVERED CODE PROVE DEFECTIVE IN ANY RESPECT, YOU (NOT THE INITIAL DEVELOPER OR ANY OTHER CONTRIBUTOR) ASSUME THE COST OF ANY NE [...]
+ .
+ 8. Termination
+ .
+ 8.1. This License and the rights granted hereunder will terminate automatically if You fail to comply with terms herein and fail to cure such breach within 30 days of becoming aware of the breach. All sublicenses to the Covered Code which are properly granted shall survive any termination of this License. Provisions which, by their nature, must remain in effect beyond the termination of this License shall survive.
+ .
+ 8.2. If You initiate litigation by asserting a patent infringement claim (excluding declatory judgment actions) against Initial Developer or a Contributor (the Initial Developer or Contributor against whom You file such action is referred to as "Participant") alleging that:
+ .
+ such Participant's Contributor Version directly or indirectly infringes any patent, then any and all rights granted by such Participant to You under Sections 2.1 and/or 2.2 of this License shall, upon 60 days notice from Participant terminate prospectively, unless if within 60 days after receipt of notice You either: (i) agree in writing to pay Participant a mutually agreeable reasonable royalty for Your past and future use of Modifications made by such Participant, or (ii) withdraw You [...]
+ any software, hardware, or device, other than such Participant's Contributor Version, directly or indirectly infringes any patent, then any rights granted to You by such Participant under Sections 2.1(b) and 2.2(b) are revoked effective as of the date You first made, used, sold, distributed, or had made, Modifications made by that Participant.
+ 8.3. If You assert a patent infringement claim against Participant alleging that such Participant's Contributor Version directly or indirectly infringes any patent where such claim is resolved (such as by license or settlement) prior to the initiation of patent infringement litigation, then the reasonable value of the licenses granted by such Participant under Sections 2.1 or 2.2 shall be taken into account in determining the amount or value of any payment or license.
+ .
+ 8.4. In the event of termination under Sections 8.1 or 8.2 above, all end user license agreements (excluding distributors and resellers) which have been validly granted by You or any distributor hereunder prior to termination shall survive termination.
+ .
+ 9. LIMITATION OF LIABILITY
+ .
+ UNDER NO CIRCUMSTANCES AND UNDER NO LEGAL THEORY, WHETHER TORT (INCLUDING NEGLIGENCE), CONTRACT, OR OTHERWISE, SHALL YOU, THE INITIAL DEVELOPER, ANY OTHER CONTRIBUTOR, OR ANY DISTRIBUTOR OF COVERED CODE, OR ANY SUPPLIER OF ANY OF SUCH PARTIES, BE LIABLE TO ANY PERSON FOR ANY INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES OF ANY CHARACTER INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER COMMERCIAL D [...]
+ .
+ 10. U.S. government end users
+ .
+ The Covered Code is a "commercial item," as that term is defined in 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer software" and "commercial computer software documentation," as such terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all U.S. Government End Users acquire Covered Code with only those rights set forth herein.
+ .
+ 11. Miscellaneous
+ .
+ This License represents the complete agreement concerning subject matter hereof. If any provision of this License is held to be unenforceable, such provision shall be reformed only to the extent necessary to make it enforceable. This License shall be governed by California law provisions (except to the extent applicable law, if any, provides otherwise), excluding its conflict-of-law provisions. With respect to disputes in which at least one party is a citizen of, or an entity chartered [...]
+ .
+ 12. Responsibility for claims
+ .
+ As between Initial Developer and the Contributors, each party is responsible for claims and damages arising, directly or indirectly, out of its utilization of rights under this License and You agree to work with Initial Developer and Contributors to distribute such responsibility on an equitable basis. Nothing herein is intended or shall be deemed to constitute any admission of liability.
+ .
+ Includes Protocol Buffers licensed under terms:
+ Redistribution and use in source and binary forms, with or without modification, are
+ permitted provided that the following conditions are met:
+ .
+ 1. Redistributions of source code must retain the above copyright notice, this list of
+ conditions and the following disclaimer.
+ .
+ 2. Redistributions in binary form must reproduce the above copyright notice, this list
+ of conditions and the following disclaimer in the documentation and/or other materials
+ provided with the distribution.
+ .
+ THIS SOFTWARE IS PROVIDED BY <COPYRIGHT HOLDER> ``AS IS'' AND ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> OR
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ .
+ The views and conclusions contained in the software and documentation are those of the
+ authors and should not be interpreted as representing official policies, either expressed
+ or implied, of <copyright holder>
+
+Files: debian/*
+Copyright: 2015 Olivier Sallou <osallou at debian.org>
+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".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
+# Please avoid to pick license terms that are more restrictive than the
+# packaged work, as it may make Debian's contributions unacceptable upstream.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..f1db997
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+README.txt
+README.txt
+requirements.txt
diff --git a/debian/init.d.ex b/debian/init.d.ex
new file mode 100644
index 0000000..8e5cc3e
--- /dev/null
+++ b/debian/init.d.ex
@@ -0,0 +1,166 @@
+#!/bin/sh
+### BEGIN INIT INFO
+# Provides: obitools
+# Required-Start: $local_fs $network $remote_fs $syslog
+# Required-Stop: $local_fs $network $remote_fs $syslog
+# Default-Start: 2 3 4 5
+# Default-Stop: 0 1 6
+# Short-Description: <Enter a short description of the software>
+# Description: <Enter a long description of the software>
+# <...>
+# <...>
+### END INIT INFO
+
+# Author: Olivier Sallou <osallou at debian.org>
+
+# Do NOT "set -e"
+
+# PATH should only include /usr/* if it runs after the mountnfs.sh script
+PATH=/sbin:/usr/sbin:/bin:/usr/bin
+DESC="obitools"
+NAME=obitools
+DAEMON=/usr/sbin/obitools
+DAEMON_ARGS=""
+PIDFILE=/var/run/$NAME.pid
+SCRIPTNAME=/etc/init.d/$NAME
+
+# Exit if the package is not installed
+[ -x "$DAEMON" ] || exit 0
+
+# Read configuration variable file if it is present
+[ -r /etc/default/$NAME ] && . /etc/default/$NAME
+
+# Load the VERBOSE setting and other rcS variables
+. /lib/init/vars.sh
+
+# Define LSB log_* functions.
+# Depend on lsb-base (>= 3.2-14) to ensure that this file is present
+# and status_of_proc is working.
+. /lib/lsb/init-functions
+
+#
+# Function that starts the daemon/service
+#
+do_start()
+{
+ # Return
+ # 0 if daemon has been started
+ # 1 if daemon was already running
+ # 2 if daemon could not be started
+ start-stop-daemon --start --quiet --pidfile $PIDFILE --exec $DAEMON --test > /dev/null \
+ || return 1
+ start-stop-daemon --start --quiet --pidfile $PIDFILE --exec $DAEMON -- \
+ $DAEMON_ARGS \
+ || return 2
+ # The above code will not work for interpreted scripts, use the next
+ # six lines below instead (Ref: #643337, start-stop-daemon(8) )
+ #start-stop-daemon --start --quiet --pidfile $PIDFILE --startas $DAEMON \
+ # --name $NAME --test > /dev/null \
+ # || return 1
+ #start-stop-daemon --start --quiet --pidfile $PIDFILE --startas $DAEMON \
+ # --name $NAME -- $DAEMON_ARGS \
+ # || return 2
+
+ # Add code here, if necessary, that waits for the process to be ready
+ # to handle requests from services started subsequently which depend
+ # on this one. As a last resort, sleep for some time.
+}
+
+#
+# Function that stops the daemon/service
+#
+do_stop()
+{
+ # Return
+ # 0 if daemon has been stopped
+ # 1 if daemon was already stopped
+ # 2 if daemon could not be stopped
+ # other if a failure occurred
+ start-stop-daemon --stop --quiet --retry=TERM/30/KILL/5 --pidfile $PIDFILE --name $NAME
+ RETVAL="$?"
+ [ "$RETVAL" = 2 ] && return 2
+ # Wait for children to finish too if this is a daemon that forks
+ # and if the daemon is only ever run from this initscript.
+ # If the above conditions are not satisfied then add some other code
+ # that waits for the process to drop all resources that could be
+ # needed by services started subsequently. A last resort is to
+ # sleep for some time.
+ start-stop-daemon --stop --quiet --oknodo --retry=0/30/KILL/5 --exec $DAEMON
+ [ "$?" = 2 ] && return 2
+ # Many daemons don't delete their pidfiles when they exit.
+ rm -f $PIDFILE
+ return "$RETVAL"
+}
+
+#
+# Function that sends a SIGHUP to the daemon/service
+#
+do_reload() {
+ #
+ # If the daemon can reload its configuration without
+ # restarting (for example, when it is sent a SIGHUP),
+ # then implement that here.
+ #
+ start-stop-daemon --stop --signal 1 --quiet --pidfile $PIDFILE --name $NAME
+ return 0
+}
+
+case "$1" in
+ start)
+ [ "$VERBOSE" != no ] && log_daemon_msg "Starting $DESC" "$NAME"
+ do_start
+ case "$?" in
+ 0|1) [ "$VERBOSE" != no ] && log_end_msg 0 ;;
+ 2) [ "$VERBOSE" != no ] && log_end_msg 1 ;;
+ esac
+ ;;
+ stop)
+ [ "$VERBOSE" != no ] && log_daemon_msg "Stopping $DESC" "$NAME"
+ do_stop
+ case "$?" in
+ 0|1) [ "$VERBOSE" != no ] && log_end_msg 0 ;;
+ 2) [ "$VERBOSE" != no ] && log_end_msg 1 ;;
+ esac
+ ;;
+ status)
+ status_of_proc "$DAEMON" "$NAME" && exit 0 || exit $?
+ ;;
+ #reload|force-reload)
+ #
+ # If do_reload() is not implemented then leave this commented out
+ # and leave 'force-reload' as an alias for 'restart'.
+ #
+ #log_daemon_msg "Reloading $DESC" "$NAME"
+ #do_reload
+ #log_end_msg $?
+ #;;
+ restart|force-reload)
+ #
+ # If the "reload" option is implemented then remove the
+ # 'force-reload' alias
+ #
+ log_daemon_msg "Restarting $DESC" "$NAME"
+ do_stop
+ case "$?" in
+ 0|1)
+ do_start
+ case "$?" in
+ 0) log_end_msg 0 ;;
+ 1) log_end_msg 1 ;; # Old process is still running
+ *) log_end_msg 1 ;; # Failed to start
+ esac
+ ;;
+ *)
+ # Failed to stop
+ log_end_msg 1
+ ;;
+ esac
+ ;;
+ *)
+ #echo "Usage: $SCRIPTNAME {start|stop|restart|reload|force-reload}" >&2
+ echo "Usage: $SCRIPTNAME {start|stop|status|restart|force-reload}" >&2
+ exit 3
+ ;;
+esac
+
+:
diff --git a/debian/manpage.1.ex b/debian/manpage.1.ex
new file mode 100644
index 0000000..13e7f07
--- /dev/null
+++ b/debian/manpage.1.ex
@@ -0,0 +1,56 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" (C) Copyright 2015 Olivier Sallou <osallou at debian.org>,
+.\"
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH OBITOOLS SECTION "April 30, 2015"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+obitools \- program to do something
+.SH SYNOPSIS
+.B obitools
+.RI [ options ] " files" ...
+.br
+.B bar
+.RI [ options ] " files" ...
+.SH DESCRIPTION
+This manual page documents briefly the
+.B obitools
+and
+.B bar
+commands.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+\fBobitools\fP is a program that...
+.SH OPTIONS
+These programs follow the usual GNU command line syntax, with long
+options starting with two dashes (`-').
+A summary of options is included below.
+For a complete description, see the Info files.
+.TP
+.B \-h, \-\-help
+Show summary of options.
+.TP
+.B \-v, \-\-version
+Show version of program.
+.SH SEE ALSO
+.BR bar (1),
+.BR baz (1).
+.br
+The programs are documented fully by
+.IR "The Rise and Fall of a Fooish Bar" ,
+available via the Info system.
diff --git a/debian/manpage.sgml.ex b/debian/manpage.sgml.ex
new file mode 100644
index 0000000..4b493a7
--- /dev/null
+++ b/debian/manpage.sgml.ex
@@ -0,0 +1,154 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>FIRSTNAME</firstname>">
+ <!ENTITY dhsurname "<surname>SURNAME</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>April 30, 2015</date>">
+ <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+ allowed: see man(7), man(1). -->
+ <!ENTITY dhsection "<manvolnum>SECTION</manvolnum>">
+ <!ENTITY dhemail "<email>osallou at debian.org</email>">
+ <!ENTITY dhusername "Olivier Sallou">
+ <!ENTITY dhucpackage "<refentrytitle>OBITOOLS</refentrytitle>">
+ <!ENTITY dhpackage "obitools">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>program to do something</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+
+ <arg><option>-e <replaceable>this</replaceable></option></arg>
+
+ <arg><option>--example <replaceable>that</replaceable></option></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para>This manual page documents briefly the
+ <command>&dhpackage;</command> and <command>bar</command>
+ commands.</para>
+
+ <para>This manual page was written for the &debian; distribution
+ because the original program does not have a manual page.
+ Instead, it has documentation in the &gnu;
+ <application>Info</application> format; see below.</para>
+
+ <para><command>&dhpackage;</command> is a program that...</para>
+
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+
+ <para>These programs follow the usual &gnu; command line syntax,
+ with long options starting with two dashes (`-'). A summary of
+ options is included below. For a complete description, see the
+ <application>Info</application> files.</para>
+
+ <variablelist>
+ <varlistentry>
+ <term><option>-h</option>
+ <option>--help</option>
+ </term>
+ <listitem>
+ <para>Show summary of options.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-v</option>
+ <option>--version</option>
+ </term>
+ <listitem>
+ <para>Show version of program.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+
+ <para>bar (1), baz (1).</para>
+
+ <para>The programs are documented fully by <citetitle>The Rise and
+ Fall of a Fooish Bar</citetitle> available via the
+ <application>Info</application> system.</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (and may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+ </para>
+ <para>
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
diff --git a/debian/manpage.xml.ex b/debian/manpage.xml.ex
new file mode 100644
index 0000000..164d2e9
--- /dev/null
+++ b/debian/manpage.xml.ex
@@ -0,0 +1,291 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
+"http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
+
+<!--
+
+`xsltproc -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ /usr/share/xml/docbook/stylesheet/docbook-xsl/manpages/docbook.xsl \
+ manpage.xml'
+
+A manual page <package>.<section> will be generated. You may view the
+manual page with: nroff -man <package>.<section> | less'. A typical entry
+in a Makefile or Makefile.am is:
+
+DB2MAN = /usr/share/sgml/docbook/stylesheet/xsl/docbook-xsl/manpages/docbook.xsl
+XP = xsltproc -''-nonet -''-param man.charmap.use.subset "0"
+
+manpage.1: manpage.xml
+ $(XP) $(DB2MAN) $<
+
+The xsltproc binary is found in the xsltproc package. The XSL files are in
+docbook-xsl. A description of the parameters you can use can be found in the
+docbook-xsl-doc-* packages. Please remember that if you create the nroff
+version in one of the debian/rules file targets (such as build), you will need
+to include xsltproc and docbook-xsl in your Build-Depends control field.
+Alternatively use the xmlto command/package. That will also automatically
+pull in xsltproc and docbook-xsl.
+
+Notes for using docbook2x: docbook2x-man does not automatically create the
+AUTHOR(S) and COPYRIGHT sections. In this case, please add them manually as
+<refsect1> ... </refsect1>.
+
+To disable the automatic creation of the AUTHOR(S) and COPYRIGHT sections
+read /usr/share/doc/docbook-xsl/doc/manpages/authors.html. This file can be
+found in the docbook-xsl-doc-html package.
+
+Validation can be done using: `xmllint -''-noout -''-valid manpage.xml`
+
+General documentation about man-pages and man-page-formatting:
+man(1), man(7), http://www.tldp.org/HOWTO/Man-Page/
+
+-->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "FIRSTNAME">
+ <!ENTITY dhsurname "SURNAME">
+ <!-- dhusername could also be set to "&dhfirstname; &dhsurname;". -->
+ <!ENTITY dhusername "Olivier Sallou">
+ <!ENTITY dhemail "osallou at debian.org">
+ <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+ allowed: see man(7), man(1) and
+ http://www.tldp.org/HOWTO/Man-Page/q2.html. -->
+ <!ENTITY dhsection "SECTION">
+ <!-- TITLE should be something like "User commands" or similar (see
+ http://www.tldp.org/HOWTO/Man-Page/q2.html). -->
+ <!ENTITY dhtitle "obitools User Manual">
+ <!ENTITY dhucpackage "OBITOOLS">
+ <!ENTITY dhpackage "obitools">
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <authorgroup>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote this manpage for the Debian system.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <copyright>
+ <year>2007</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ <legalnotice>
+ <para>This manual page was written for the Debian system
+ (and may be used by others).</para>
+ <para>Permission is granted to copy, distribute and/or modify this
+ document under the terms of the GNU General Public License,
+ Version 2 or (at your option) any later version published by
+ the Free Software Foundation.</para>
+ <para>On Debian systems, the complete text of the GNU General Public
+ License can be found in
+ <filename>/usr/share/common-licenses/GPL</filename>.</para>
+ </legalnotice>
+ </refentryinfo>
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>program to do something</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <!-- These are several examples, how syntaxes could look -->
+ <arg choice="plain"><option>-e <replaceable>this</replaceable></option></arg>
+ <arg choice="opt"><option>--example=<parameter>that</parameter></option></arg>
+ <arg choice="opt">
+ <group choice="req">
+ <arg choice="plain"><option>-e</option></arg>
+ <arg choice="plain"><option>--example</option></arg>
+ </group>
+ <replaceable class="option">this</replaceable>
+ </arg>
+ <arg choice="opt">
+ <group choice="req">
+ <arg choice="plain"><option>-e</option></arg>
+ <arg choice="plain"><option>--example</option></arg>
+ </group>
+ <group choice="req">
+ <arg choice="plain"><replaceable>this</replaceable></arg>
+ <arg choice="plain"><replaceable>that</replaceable></arg>
+ </group>
+ </arg>
+ </cmdsynopsis>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <!-- Normally the help and version options make the programs stop
+ right after outputting the requested information. -->
+ <group choice="opt">
+ <arg choice="plain">
+ <group choice="req">
+ <arg choice="plain"><option>-h</option></arg>
+ <arg choice="plain"><option>--help</option></arg>
+ </group>
+ </arg>
+ <arg choice="plain">
+ <group choice="req">
+ <arg choice="plain"><option>-v</option></arg>
+ <arg choice="plain"><option>--version</option></arg>
+ </group>
+ </arg>
+ </group>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>This manual page documents briefly the
+ <command>&dhpackage;</command> and <command>bar</command>
+ commands.</para>
+ <para>This manual page was written for the Debian distribution
+ because the original program does not have a manual page.
+ Instead, it has documentation in the GNU <citerefentry>
+ <refentrytitle>info</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry> format; see below.</para>
+ <para><command>&dhpackage;</command> is a program that...</para>
+ </refsect1>
+ <refsect1 id="options">
+ <title>OPTIONS</title>
+ <para>The program follows the usual GNU command line syntax,
+ with long options starting with two dashes (`-'). A summary of
+ options is included below. For a complete description, see the
+ <citerefentry>
+ <refentrytitle>info</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry> files.</para>
+ <variablelist>
+ <!-- Use the variablelist.term.separator and the
+ variablelist.term.break.after parameters to
+ control the term elements. -->
+ <varlistentry>
+ <term><option>-e <replaceable>this</replaceable></option></term>
+ <term><option>--example=<replaceable>that</replaceable></option></term>
+ <listitem>
+ <para>Does this and that.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-h</option></term>
+ <term><option>--help</option></term>
+ <listitem>
+ <para>Show summary of options.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-v</option></term>
+ <term><option>--version</option></term>
+ <listitem>
+ <para>Show version of program.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1 id="files">
+ <title>FILES</title>
+ <variablelist>
+ <varlistentry>
+ <term><filename>/etc/foo.conf</filename></term>
+ <listitem>
+ <para>The system-wide configuration file to control the
+ behaviour of <application>&dhpackage;</application>. See
+ <citerefentry>
+ <refentrytitle>foo.conf</refentrytitle>
+ <manvolnum>5</manvolnum>
+ </citerefentry> for further details.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><filename>${HOME}/.foo.conf</filename></term>
+ <listitem>
+ <para>The per-user configuration file to control the
+ behaviour of <application>&dhpackage;</application>. See
+ <citerefentry>
+ <refentrytitle>foo.conf</refentrytitle>
+ <manvolnum>5</manvolnum>
+ </citerefentry> for further details.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1 id="environment">
+ <title>ENVIRONMENT</title>
+ <variablelist>
+ <varlistentry>
+ <term><envar>FOO_CONF</envar></term>
+ <listitem>
+ <para>If used, the defined file is used as configuration
+ file (see also <xref linkend="files"/>).</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1 id="diagnostics">
+ <title>DIAGNOSTICS</title>
+ <para>The following diagnostics may be issued
+ on <filename class="devicefile">stderr</filename>:</para>
+ <variablelist>
+ <varlistentry>
+ <term><errortext>Bad configuration file. Exiting.</errortext></term>
+ <listitem>
+ <para>The configuration file seems to contain a broken configuration
+ line. Use the <option>--verbose</option> option, to get more info.
+ </para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ <para><command>&dhpackage;</command> provides some return codes, that can
+ be used in scripts:</para>
+ <segmentedlist>
+ <segtitle>Code</segtitle>
+ <segtitle>Diagnostic</segtitle>
+ <seglistitem>
+ <seg><errorcode>0</errorcode></seg>
+ <seg>Program exited successfully.</seg>
+ </seglistitem>
+ <seglistitem>
+ <seg><errorcode>1</errorcode></seg>
+ <seg>The configuration file seems to be broken.</seg>
+ </seglistitem>
+ </segmentedlist>
+ </refsect1>
+ <refsect1 id="bugs">
+ <!-- Or use this section to tell about upstream BTS. -->
+ <title>BUGS</title>
+ <para>The program is currently limited to only work
+ with the <package>foobar</package> library.</para>
+ <para>The upstreams <acronym>BTS</acronym> can be found
+ at <ulink url="http://bugzilla.foo.tld"/>.</para>
+ </refsect1>
+ <refsect1 id="see_also">
+ <title>SEE ALSO</title>
+ <!-- In alpabetical order. -->
+ <para><citerefentry>
+ <refentrytitle>bar</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>baz</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>foo.conf</refentrytitle>
+ <manvolnum>5</manvolnum>
+ </citerefentry></para>
+ <para>The programs are documented fully by <citetitle>The Rise and
+ Fall of a Fooish Bar</citetitle> available via the <citerefentry>
+ <refentrytitle>info</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry> system.</para>
+ </refsect1>
+</refentry>
+
diff --git a/debian/menu.ex b/debian/menu.ex
new file mode 100644
index 0000000..fd38a04
--- /dev/null
+++ b/debian/menu.ex
@@ -0,0 +1,2 @@
+?package(obitools):needs="X11|text|vc|wm" section="Applications/see-menu-manual"\
+ title="obitools" command="/usr/bin/obitools"
diff --git a/debian/obitools.cron.d.ex b/debian/obitools.cron.d.ex
new file mode 100644
index 0000000..a6fc772
--- /dev/null
+++ b/debian/obitools.cron.d.ex
@@ -0,0 +1,4 @@
+#
+# Regular cron jobs for the obitools package
+#
+0 4 * * * root [ -x /usr/bin/obitools_maintenance ] && /usr/bin/obitools_maintenance
diff --git a/debian/obitools.default.ex b/debian/obitools.default.ex
new file mode 100644
index 0000000..47f0558
--- /dev/null
+++ b/debian/obitools.default.ex
@@ -0,0 +1,10 @@
+# Defaults for obitools initscript
+# sourced by /etc/init.d/obitools
+# installed at /etc/default/obitools by the maintainer scripts
+
+#
+# This is a POSIX shell fragment
+#
+
+# Additional options that are passed to the Daemon.
+DAEMON_OPTS=""
diff --git a/debian/obitools.doc-base.EX b/debian/obitools.doc-base.EX
new file mode 100644
index 0000000..e206174
--- /dev/null
+++ b/debian/obitools.doc-base.EX
@@ -0,0 +1,20 @@
+Document: obitools
+Title: Debian obitools Manual
+Author: <insert document author here>
+Abstract: This manual describes what obitools is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/obitools/obitools.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/obitools/obitools.ps.gz
+
+Format: text
+Files: /usr/share/doc/obitools/obitools.text.gz
+
+Format: HTML
+Index: /usr/share/doc/obitools/html/index.html
+Files: /usr/share/doc/obitools/html/*.html
diff --git a/debian/patches/fix_path_interpreter b/debian/patches/fix_path_interpreter
new file mode 100644
index 0000000..5a93ac9
--- /dev/null
+++ b/debian/patches/fix_path_interpreter
@@ -0,0 +1,315 @@
+Subject: wrong interpreter path
+Description: use Debian Python
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2015-04-30
+Forwarded: no
+--- a/src/extractreads.py
++++ b/src/extractreads.py
+@@ -1,3 +1,4 @@
++#!/usr/bin/python
+ '''
+ Created on 9 juin 2012
+
+--- a/src/extractreads2.py
++++ b/src/extractreads2.py
+@@ -1,3 +1,4 @@
++#!/usr/bin/python
+ '''
+ Created on 9 juin 2012
+
+--- a/src/ali2consensus.py
++++ b/src/ali2consensus.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+
+ '''
+ Created on 30 sept. 2011
+--- a/src/ecodbtaxstat.py
++++ b/src/ecodbtaxstat.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`ecodbtaxstat`: gives taxonomic rank frequency of a given ``ecopcr`` database
+ =====================================================================================
+--- a/src/ecotag.py
++++ b/src/ecotag.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`ecotag`: assigns sequences to taxa
+ ===========================================
+--- a/src/ecotaxspecificity.py
++++ b/src/ecotaxspecificity.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`ecotaxspecificity`: Evaluates barcode resolution
+ =========================================================
+--- a/src/ecotaxstat.py
++++ b/src/ecotaxstat.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`ecotaxstat` : getting the coverage of an ecoPCR output compared to the original ecoPCR database
+ ========================================================================================================
+--- a/src/illuminapairedend.py
++++ b/src/illuminapairedend.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`illuminapairedend`: aligns paired-end Illumina reads
+ =============================================================
+--- a/src/ngsfilter.py
++++ b/src/ngsfilter.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`ngsfilter` : Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers
+ ===================================================================================================================
+--- a/src/obiaddtaxids.py
++++ b/src/obiaddtaxids.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obiaddtaxids`: adds *taxids* to sequence records using an ecopcr database
+ ==================================================================================
+--- a/src/obiannotate.py
++++ b/src/obiannotate.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+
+ '''
+ :py:mod:`obiannotate`: adds/edits sequence record annotations
+--- a/src/obiclean.py
++++ b/src/obiclean.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+
+ '''
+ :py:mod:`obiclean`: tags a set of sequences for PCR/sequencing errors identification
+--- a/src/obicomplement.py
++++ b/src/obicomplement.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ """
+ :py:mod:`obicomplement`: reverse-complements sequences
+ ======================================================
+--- a/src/obiconvert.py
++++ b/src/obiconvert.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obiconvert`: converts sequence files to different output formats
+ =========================================================================
+--- a/src/obicount.py
++++ b/src/obicount.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obicount`: counts the number of sequence records
+ =========================================================
+--- a/src/obicut.py
++++ b/src/obicut.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obicut`: trims sequences
+ =================================
+--- a/src/obidistribute.py
++++ b/src/obidistribute.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obidistribute`: Distributes sequence records over several sequence records files
+ =========================================================================================
+--- a/src/obiextract.py
++++ b/src/obiextract.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obiextract`: extract samples from a dataset
+ ====================================================
+--- a/src/obigrep.py
++++ b/src/obigrep.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obigrep`: filters sequence file
+ ========================================
+--- a/src/obihead.py
++++ b/src/obihead.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obihead`: extracts the first sequence records
+ ======================================================
+--- a/src/obijoinpairedend.py
++++ b/src/obijoinpairedend.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obijoinpairedend`: Joins paired-end reads
+ ==================================================
+--- a/src/obipr2.py
++++ b/src/obipr2.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obipr2`: converts silva database into an ecoPCR database
+ =================================================================
+--- a/src/obisample.py
++++ b/src/obisample.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obisample`: randomly resamples sequence records
+ ========================================================
+--- a/src/obiselect.py
++++ b/src/obiselect.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ """
+ :py:mod:`obiselect` : selects representative sequence records
+ =============================================================
+--- a/src/obisilva.py
++++ b/src/obisilva.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obisilva`: converts silva database into an ecoPCR database
+ ===================================================================
+--- a/src/obisort.py
++++ b/src/obisort.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obisort`: Sorts sequence records according to the value of a given attribute
+ =====================================================================================
+--- a/src/obisplit.py
++++ b/src/obisplit.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obisplit`: Splits a sequence file in a set of subfiles
+ ===============================================================
+--- a/src/obistat.py
++++ b/src/obistat.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obistat`: computes basic statistics for attribute values
+ =================================================================
+--- a/src/obitab.py
++++ b/src/obitab.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obitab`: converts a sequence file to a tabular file
+ ============================================================
+--- a/src/obitail.py
++++ b/src/obitail.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obitail`: extracts the last sequence records
+ =====================================================
+--- a/src/obitaxonomy.py
++++ b/src/obitaxonomy.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obitaxonomy`: manages taxonomic databases
+ ==================================================
+--- a/src/obiuniq.py
++++ b/src/obiuniq.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`obiuniq`: groups and dereplicates sequences
+ ====================================================
+--- a/src/oligotag.py
++++ b/src/oligotag.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ :py:mod:`oligotag`: Designs a set of oligonucleotides with specified properties
+ ===============================================================================
+--- a/src/obitools/barcodecoverage/calcBc.py
++++ b/src/obitools/barcodecoverage/calcBc.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ Created on 24 nov. 2011
+
+--- a/src/obitools/barcodecoverage/drawBcTree.py
++++ b/src/obitools/barcodecoverage/drawBcTree.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ Created on 25 nov. 2011
+
+--- a/src/obitools/barcodecoverage/findErrors.py
++++ b/src/obitools/barcodecoverage/findErrors.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ Created on 24 nov. 2011
+
+--- a/src/obitools/barcodecoverage/readFiles.py
++++ b/src/obitools/barcodecoverage/readFiles.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ Created on 23 nov. 2011
+
+--- a/src/obitools/barcodecoverage/writeBcTree.py
++++ b/src/obitools/barcodecoverage/writeBcTree.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ Created on 25 nov. 2011
+
+--- a/src/obitools/solexaPairEnd.py
++++ b/src/obitools/solexaPairEnd.py
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python
++#!/usr/bin/python
+ '''
+ Created on 30 dec. 2009
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..1a4ce68
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+use_debian_libs
+fix_path_interpreter
diff --git a/debian/patches/use_debian_libs b/debian/patches/use_debian_libs
new file mode 100644
index 0000000..3777672
--- /dev/null
+++ b/debian/patches/use_debian_libs
@@ -0,0 +1,82 @@
+Subject: skip virtualenv installation
+Description: installer uses pip and virtualenv for install,
+ this patch removes this specific install to install in Debian dirs
+ and use Debian libs
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2015-04-30
+Forwarded: no
+--- a/distutils.ext/obidistutils/serenity/__init__.py
++++ b/distutils.ext/obidistutils/serenity/__init__.py
+@@ -63,7 +63,7 @@
+
+ log.info("%s will be installed with python : %s" % (package,virtualpython))
+
+- if install_requirements():
++ if install_requirements(False):
+ log.info("Restarting installation with all dependencies ok")
+ rerun_with_anothe_python(virtualpython)
+
+--- a/distutils.ext/obidistutils/serenity/checkpackage.py
++++ b/distutils.ext/obidistutils/serenity/checkpackage.py
+@@ -15,48 +15,7 @@
+ from obidistutils.serenity.checkpip import get_a_pip_module
+
+ def is_installed(requirement,pip=None):
+-
+- if pip is None:
+- pip = get_a_pip_module()
+-
+- get_installed_distributions=pip.util.get_installed_distributions
+-
+- requirement_project,requirement_relation,requirement_version = parse_package_requirement(requirement)
+-
+- package = [x for x in get_installed_distributions() if x.project_name==requirement_project]
+-
+- if len(package)==1:
+- if requirement_version is not None and requirement_relation is not None:
+- rep = (len(package)==1) and eval("StrictVersion('%s') %s StrictVersion('%s')" % (package[0].version,
+- requirement_relation,
+- requirement_version)
+- )
+- else:
+- rep=True
+- else:
+- rep=False
+-
+- if rep:
+- if requirement_version is not None and requirement_relation is not None:
+- log.info("Look for package %s (%s%s) : ok version %s installed" % (requirement_project,
+- requirement_relation,
+- requirement_version,
+- package[0].version))
+- else:
+- log.info("Look for package %s : ok version %s installed" % (requirement_project,
+- package[0].version))
+- else:
+- if len(package)!=1:
+- log.info("Look for package %s (%s%s) : not installed" % (requirement_project,
+- requirement_relation,
+- requirement_version))
+- else:
+- log.info("Look for package %s (%s%s) : failed only version %s installed" % (requirement_project,
+- requirement_relation,
+- requirement_version,
+- package[0].version))
+-
+- return rep
++ return True
+
+
+ def get_requirements(pip=None):
+--- a/setup.py
++++ b/setup.py
+@@ -66,7 +66,7 @@
+ license=LICENSE,
+ url=URL,
+ python_src=SRC,
+- sse='sse2',
+- serenity=serenity)
++ sse='sse2')
++ #serenity=serenity)
+
+
diff --git a/debian/postinst.ex b/debian/postinst.ex
new file mode 100644
index 0000000..9616341
--- /dev/null
+++ b/debian/postinst.ex
@@ -0,0 +1,39 @@
+#!/bin/sh
+# postinst script for obitools
+#
+# 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)
+ ;;
+
+ 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.ex b/debian/postrm.ex
new file mode 100644
index 0000000..ea86ed4
--- /dev/null
+++ b/debian/postrm.ex
@@ -0,0 +1,37 @@
+#!/bin/sh
+# postrm script for obitools
+#
+# 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|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
diff --git a/debian/preinst.ex b/debian/preinst.ex
new file mode 100644
index 0000000..26d5644
--- /dev/null
+++ b/debian/preinst.ex
@@ -0,0 +1,35 @@
+#!/bin/sh
+# preinst script for obitools
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+# * <new-preinst> `install'
+# * <new-preinst> `install' <old-version>
+# * <new-preinst> `upgrade' <old-version>
+# * <old-preinst> `abort-upgrade' <new-version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+ install|upgrade)
+ ;;
+
+ abort-upgrade)
+ ;;
+
+ *)
+ echo "preinst 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/prerm.ex b/debian/prerm.ex
new file mode 100644
index 0000000..2269939
--- /dev/null
+++ b/debian/prerm.ex
@@ -0,0 +1,38 @@
+#!/bin/sh
+# prerm script for obitools
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+# * <prerm> `remove'
+# * <old-prerm> `upgrade' <new-version>
+# * <new-prerm> `failed-upgrade' <old-version>
+# * <conflictor's-prerm> `remove' `in-favour' <package> <new-version>
+# * <deconfigured's-prerm> `deconfigure' `in-favour'
+# <package-being-installed> <version> `removing'
+# <conflicting-package> <version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+ remove|upgrade|deconfigure)
+ ;;
+
+ failed-upgrade)
+ ;;
+
+ *)
+ echo "prerm 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/python-obitools.doc-base b/debian/python-obitools.doc-base
new file mode 100644
index 0000000..eaf9f99
--- /dev/null
+++ b/debian/python-obitools.doc-base
@@ -0,0 +1,9 @@
+Document: python-obitools
+Title: OBITools manual
+Author: Eric coissac
+Abstract: This manual describes OBITools and its tools
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/python-obitools/html/index.html
+Files: /usr/share/doc/python-obitools/html/*.html
diff --git a/debian/python-obitools.install b/debian/python-obitools.install
new file mode 100644
index 0000000..528c935
--- /dev/null
+++ b/debian/python-obitools.install
@@ -0,0 +1 @@
+build/sphinx/html usr/share/doc/python-obitools
diff --git a/debian/python-obitools.links b/debian/python-obitools.links
new file mode 100644
index 0000000..f95a35b
--- /dev/null
+++ b/debian/python-obitools.links
@@ -0,0 +1,3 @@
+usr/share/doc/python-obitools/html/_sources usr/share/doc/python-obitools/rst
+#usr/share/doc/python-obitools/html/_static/jquery.js usr/share/javascript/jquery/jquery.js
+#usr/share/doc/python-obitools/html/_static/underscore.js usr/share/javascript/underscore/underscore.js
diff --git a/debian/python-obitools.manpages b/debian/python-obitools.manpages
new file mode 100644
index 0000000..90766e9
--- /dev/null
+++ b/debian/python-obitools.manpages
@@ -0,0 +1 @@
+build/sphinx/man/*.1
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..41afd39
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,42 @@
+#!/usr/bin/make -f
+# See debhelper(7) (uncomment to enable)
+# output every command that modifies files on the build system.
+#DH_VERBOSE = 1
+
+# see EXAMPLES in dpkg-buildflags(1) and read /usr/share/dpkg/*
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+# see FEATURE AREAS in dpkg-buildflags(1)
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+# see ENVIRONMENT in dpkg-buildflags(1)
+# package maintainers to append CFLAGS
+#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
+# package maintainers to append LDFLAGS
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+export PYBUILD_NAME=obitools
+
+
+# main packaging script based on dh7 syntax
+%:
+ dh $@ --with python2,sphinxdoc
+
+# debmake generated override targets
+# This is example for Cmake (See http://bugs.debian.org/641051 )
+#override_dh_auto_configure:
+# dh_auto_configure -- \
+# -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH)
+
+override_dh_install:
+ dh_install
+# rm debian/python-obitools/usr/share/doc/python-obitools/html/_static/jquery.js
+# rm debian/python-obitools/usr/share/doc/python-obitools/html/_static/underscore.js
+
+
+override_dh_clean:
+ dh_clean
+ rm -rf build
+ rm -f doc/sphinx/build_dir.txt
+
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/watch b/debian/watch
new file mode 100644
index 0000000..3f37a05
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts=dversionmangle=s/\+dfsg//,uversionmangle=s/(rc|a|b|c)/~$1/ \
+http://pypi.debian.net/OBITools/OBITools-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/obitools.git
More information about the debian-med-commit
mailing list