Author: osallou Date: 2014-08-19 06:53:11 +0000 (Tue, 19 Aug 2014) New Revision: 17782
Added: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/changelog trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/control trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/copyright trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/docs trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.install trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.manpages trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/add_hardening trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/series trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/use_debian_libs trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/rules Removed: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/changelog trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/control trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/copyright trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/docs trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.install trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.manpages trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/series trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/rules Log: [svn-buildpackage] Tagging mapsembler2 2.2.1+dfsg-1 Deleted: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/changelog =================================================================== --- trunk/packages/mapsembler2/trunk/debian/changelog 2014-08-18 13:32:39 UTC (rev 17763) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/changelog 2014-08-19 06:53:11 UTC (rev 17782) @@ -1,30 +0,0 @@ -mapsembler2 (2.1.6+dfsg-1) unstable; urgency=medium - - * New upstream release - - -- Olivier Sallou <[email protected]> Thu, 29 May 2014 15:07:28 +0200 - -mapsembler2 (2.1.2+dfsg-1) unstable; urgency=low - - * New upstream release - - -- Olivier Sallou <[email protected]> Fri, 21 Feb 2014 15:42:22 +0100 - -mapsembler2 (2.0.31-1) unstable; urgency=low - - * New upstream release - - -- Olivier Sallou <[email protected]> Fri, 21 Feb 2014 15:13:29 +0100 - -mapsembler2 (2.0.5+dfsg-2) unstable; urgency=low - - * d/control: Add missing build dep - - -- Olivier Sallou <[email protected]> Thu, 06 Feb 2014 08:06:55 +0100 - -mapsembler2 (2.0.5+dfsg-1) unstable; urgency=medium - - * First debian package (Closes: #737099). - - -- Olivier Sallou <[email protected]> Sat, 01 Feb 2014 16:55:29 +0100 - Copied: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/changelog (from rev 17778, trunk/packages/mapsembler2/trunk/debian/changelog) =================================================================== --- trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/changelog (rev 0) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/changelog 2014-08-19 06:53:11 UTC (rev 17782) @@ -0,0 +1,31 @@ +mapsembler2 (2.2.1+dfsg-1) unstable; urgency=medium + + * New upstream release + Change of license to AGPL-3 + + -- Olivier Sallou <[email protected]> Thu, 29 May 2014 15:07:28 +0200 + +mapsembler2 (2.1.2+dfsg-1) unstable; urgency=low + + * New upstream release + + -- Olivier Sallou <[email protected]> Fri, 21 Feb 2014 15:42:22 +0100 + +mapsembler2 (2.0.31-1) unstable; urgency=low + + * New upstream release + + -- Olivier Sallou <[email protected]> Fri, 21 Feb 2014 15:13:29 +0100 + +mapsembler2 (2.0.5+dfsg-2) unstable; urgency=low + + * d/control: Add missing build dep + + -- Olivier Sallou <[email protected]> Thu, 06 Feb 2014 08:06:55 +0100 + +mapsembler2 (2.0.5+dfsg-1) unstable; urgency=medium + + * First debian package (Closes: #737099). + + -- Olivier Sallou <[email protected]> Sat, 01 Feb 2014 16:55:29 +0100 + Deleted: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/control =================================================================== --- trunk/packages/mapsembler2/trunk/debian/control 2014-08-18 13:32:39 UTC (rev 17763) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/control 2014-08-19 06:53:11 UTC (rev 17782) @@ -1,34 +0,0 @@ -Source: mapsembler2 -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Olivier Sallou <[email protected]> -Section: science -Priority: optional -Build-Depends: debhelper (>= 9), - bc, zlib1g-dev, help2man -Standards-Version: 3.9.5 -Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mapsembler2/trunk/ -Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mapsembler2/trunk/ -Homepage: http://colibread.inria.fr/mapsembler2/ - -Package: mapsembler2 -Architecture: any -Depends: ${misc:Depends}, ${shlibs:Depends}, - zlib1g, bc -Description: bioinformatics targeted assembly software - Mapsembler2 is a targeted assembly software. - It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) - and a set of input sequences (starters). - . - It first determines if each starter is read-coherent, e.g. whether reads - confirm the presence of each starter in the original sequence. - Then for each read-coherent starter, Mapsembler2 outputs its sequence - neighborhood as a linear sequence or as a graph, depending on the user choice. - . - Mapsembler2 may be used for (not limited to): - - Validate an assembled sequence (input as starter), e.g. from a de - Bruijn graph assembly where read-coherence was not enforced. - - Checks if a gene (input as starter) has an homolog in a set of reads - - Checks if a known enzyme is present in a metagenomic NGS read set. - - Enrich unmappable reads by extending them, possibly making them mappable - - Checks what happens at the extremities of a contig - - Remove contaminants or symbiont reads from a read set Copied: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/control (from rev 17777, trunk/packages/mapsembler2/trunk/debian/control) =================================================================== --- trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/control (rev 0) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/control 2014-08-19 06:53:11 UTC (rev 17782) @@ -0,0 +1,34 @@ +Source: mapsembler2 +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Olivier Sallou <[email protected]> +Section: science +Priority: optional +Build-Depends: debhelper (>= 9), cmake, + bc, zlib1g-dev, help2man, libhdf5-dev, libcppunit-dev, libboost-dev +Standards-Version: 3.9.5 +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mapsembler2/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mapsembler2/trunk/ +Homepage: http://colibread.inria.fr/mapsembler2/ + +Package: mapsembler2 +Architecture: any +Depends: ${misc:Depends}, ${shlibs:Depends}, + zlib1g, bc +Description: bioinformatics targeted assembly software + Mapsembler2 is a targeted assembly software. + It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) + and a set of input sequences (starters). + . + It first determines if each starter is read-coherent, e.g. whether reads + confirm the presence of each starter in the original sequence. + Then for each read-coherent starter, Mapsembler2 outputs its sequence + neighborhood as a linear sequence or as a graph, depending on the user choice. + . + Mapsembler2 may be used for (not limited to): + - Validate an assembled sequence (input as starter), e.g. from a de + Bruijn graph assembly where read-coherence was not enforced. + - Checks if a gene (input as starter) has an homolog in a set of reads + - Checks if a known enzyme is present in a metagenomic NGS read set. + - Enrich unmappable reads by extending them, possibly making them mappable + - Checks what happens at the extremities of a contig + - Remove contaminants or symbiont reads from a read set Deleted: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/copyright =================================================================== --- trunk/packages/mapsembler2/trunk/debian/copyright 2014-08-18 13:32:39 UTC (rev 17763) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/copyright 2014-08-19 06:53:11 UTC (rev 17782) @@ -1,550 +0,0 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Upstream-Name: mapsembler2 -Source: http://colibread.inria.fr/mapsembler2 -Files-Excluded: - visu - results_visualization - -License: CeCILL - This Agreement is a free software license that is the result of discussions - between its authors in order to ensure compliance with the two main - principles guiding its drafting: - - firstly, its conformity with French law, both as regards the law of - torts and intellectual property law, and the protection that it offers - to authors and the holders of economic rights over software. - - secondly, compliance with the principles for the distribution of free - software: access to source codes, extended user-rights. - . - The following bodies are the authors of this license CeCILL (Ce : CEA, C : - CNRS, I : INRIA, LL : Logiciel Libre): - . - Commissariat à l'Energie Atomique - CEA, a public scientific, technical and - industrial establishment, having its principal place of business at 31-33 - rue de la Fédération, 75752 PARIS cedex 15, 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. - . - . - PREAMBLE - -------- - . - . - The purpose of this Free Software Licensing 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 ensure that this status is retained for subsequent - redistribution operations. - . - As a counterpart to the access to the source code and 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, it is brought to the user's attention that the risks - associated with loading, using, modifying and/or developing or reproducing - the software by the user given its nature of Free Software, that may - mean that it is complicated to manipulate, and that also therefore means - that it is reserved for developers and experienced professionals having - in-depth computer knowledge. Users are therefore encouraged to load and test - the Software's suitability 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 Articles 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 operation thereof to its provisions. - . - . - Article 1 - DEFINITIONS - ------------------------ - . - . - For the purposes of this Agreement, when the following expressions commence - with a capital letter, they shall have the following meaning: - . - Agreement: means this Licensing Agreement, and any or all of its subsequent - versions. - . - Software: means the software in its Object Code and/or Source Code form - and, where applicable, its documentation, "as is" at the time when the - Licensee accepts the Agreement. - . - Initial Software: means the Software in its Source Code and/or Object Code - form and, where applicable, its documentation, "as is" at the time when it - is distributed for the first time 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 of the economic rights over the Initial - Software. - . - Licensee(s): mean(s) the Software user(s) having accepted the Agreement. - . - Contributor: means a Licensee having made at least one Contribution. - . - Licensor: means the Holder, or any or all other individual or legal entity, - that distributes the Software under the Agreement. - . - Contributions: mean any or all modifications, corrections, translations, - adaptations and/or new functionalities integrated into the Software by any - or all Contributor, and the Static Modules. - . - Module: means a set of sources files including their documentation that, - once compiled in executable form, enables supplementary functionalities or - services to be developed in addition to those offered by the Software. - . - Dynamic Module: means any or all module, created by the Contributor, that - is independent of the Software, so that this module and the Software are in - two different executable forms that are run in separate address spaces, - with one calling the other when they are run. - . - Static Module: means any or all module, created by the Contributor and - connected to the Software by a static link that makes their object codes - interdependent. This module and the Software to which it is connected, are - combined in a single executable. - . - 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 to enable the Licensor to grant the - Licensee a free, non-exclusive, transferable and worldwide License for the - Software as set forth in Article 5 hereinafter for the whole term of - protection of 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 by 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 - specific nature of the Software, to the limited warranty, and to the - limitation to use by 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 is aware thereof. - . - . - 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 during the whole legal term of - protection of the economic rights over the Software. - . - . - Article 5 - SCOPE OF THE RIGHTS GRANTED - --------------------------------------- - . - . - The Licensor hereby grants to the Licensee, that accepts such, the - following rights as regards 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. - . - Otherwise, the Licensor grants to the Licensee free of charge exploitation - rights on the patents he holds on whole or part of the inventions - implemented in the Software. - . - 5.1. RIGHTS OF USE - . - The Licensee is authorized to use the Software, unrestrictedly, as regards - the fields of application, with it being hereinafter specified that this - relates to: - - permanent or temporary reproduction of all or part of the Software by - any or all means and in any or all form. - - loading, displaying, running, or storing the Software on any or all - medium. - - entitlement to observe, study or test the operation thereof so as to - establish the ideas and principles that form the basis for 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 modification to the Software, and the right to - reproduce the resulting Software. - . - The Licensee is authorized to make any or all Contribution to the Software - provided that it explicitly mentions its name as the author of said - Contribution and the date of the development thereof. - . - 5.3. DISTRIBUTION AND PUBLICATION RIGHTS - . - In particular, the right of distribution and publication includes the right - to 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, a copy or copies of the Software - by means of any or all process. - The Licensee is further authorized to redistribute copies of the modified - or unmodified Software to third parties according to the terms and - conditions set forth hereinafter. - . - 5.3.1. REDISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION - . - The Licensee is authorized to redistribute true copies of the Software in - Source Code or Object Code form, provided that said redistribution complies - with all the provisions of the Agreement and is accompanied by: - - a copy of the Agreement, - - 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 Software's Object Code is - redistributed, the Licensee allows future Licensees unhindered access to - the Software's full Source Code by providing them with the terms and - conditions for access thereto, it being understood that the additional cost - of acquiring the Source Code shall not exceed the cost of transferring the - data. - . - 5.3.2. REDISTRIBUTION OF MODIFIED SOFTWARE - . - When the Licensee makes a Contribution to the Software, the terms and - conditions for the redistribution of the Modified Software shall then be - subject to all the provisions hereof. - . - The Licensee is authorized to redistribute the Modified Software, in Source - Code or Object Code form, provided that said redistribution complies with - all the provisions of the Agreement and is accompanied by: - - a copy of the Agreement, - - 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 Modified Software's Object Code is - redistributed, the Licensee allows future Licensees unhindered access to - the Modified Software's full Source Code by providing them with the terms - and conditions for access thereto, it being understood that the additional - cost of acquiring the Source Code shall not exceed the cost of transferring - the data. - . - . - 5.3.3. redistribution OF DYNAMIC MODULES - . - When the Licensee has developed a Dynamic Module, the terms and conditions - hereof do not apply to said Dynamic Module, that may be distributed under - a separate Licensing Agreement. - . - 5.3.4. COMPATIBILITY WITH THE GPL LICENSE - . - In the event that the Modified or unmodified Software is included in a code - that is subject to the provisions of the GPL License, the Licensee is - authorized to redistribute the whole under the GPL License. - . - In the event that the Modified Software includes a code that is subject to - the provisions of the GPL License, the Licensee is authorized to - redistribute the Modified Software under the GPL License. - . - . - 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 and it shall have sole entitlement to modify the - terms and conditions for the distribution of said Initial Software. - . - The Holder undertakes to maintain the distribution of the Initial Software - under the conditions of the Agreement, for the duration set forth in - article 4.2.. - . - 6.2. OVER THE CONTRIBUTIONS - . - The intellectual property rights over the Contributions belong to the - holder of the economic rights as designated by effective legislation. - . - 6.3. OVER THE DYNAMIC MODULES - . - The Licensee having developed a Dynamic Module is the holder of the - intellectual property rights over said Dynamic Module and is free to choose - the agreement that shall govern its distribution. - . - 6.4. JOINT PROVISIONS - . - 6.4.1. The Licensee expressly undertakes: - - not to remove, or modify, in any or all manner, the intellectual - property notices affixed to the Software; - - to reproduce said notices, in an identical manner, in the copies of - the Software. - . - 6.4.2. The Licensee undertakes not to directly or indirectly infringe the - intellectual property rights of the Holder and/or Contributors and to take, - where applicable, vis-à-vis its staff, any or all measures required to - ensure respect for 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 service. The - terms and conditions of such technical assistance, and/or such - maintenance, shall then 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 or all Licensor shall be entitled to offer to its - Licensees, under its own 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 shall decide upon - itself. Said warranty, and the financial terms and conditions of its - application, shall be subject to a separate instrument executed between the - Licensor and the Licensee. - . - . - Article 8 - LIABILITY - ---------------------- - . - . - 8.1. Subject to the provisions of Article 8.2, should the Licensor fail to - fulfill all or part of its obligations hereunder, the Licensee shall be - entitled to claim compensation for the direct loss suffered as a result of - a fault on the part of the Licensor, subject to providing evidence of it. - . - 8.2. The Licensor's liability is limited to the commitments made under this - Licensing Agreement and shall not be incurred as a result , in particular: - (i) of loss due the Licensee's total or partial failure to fulfill its - obligations, (ii) direct or consequential loss due to the Software's use or - performance that is suffered by the Licensee, when the latter is a - professional using said Software for professional purposes and (iii) - consequential loss due to the Software's use or performance. 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 current situation as regards - scientific and technical know-how at the time when the Software was - distributed did not enable all possible uses to be tested and verified, nor - for the presence of any or all faults 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 that are - reserved for experienced users. - . - The Licensee shall be responsible for verifying, by any or all means, the - product's suitability for its requirements, its due and proper functioning, - and for ensuring that it shall not cause damage to either persons or - property. - . - 9.2. The Licensor hereby represents, in good faith, that it is entitled to - grant all the rights on the Software (including in particular the rights - set forth in Article 5 hereof over the Software). - . - 9.3. The Licensee acknowledges that the Software is supplied "as is" by the - Licensor without any or all other express or tacit warranty, other than - that provided for in Article 9.2 and, in particular, without any or all - warranty as to its market value, its secured, innovative or relevant - nature. - . - Specifically, the Licensor does not warrant that the Software is free from - any or all error, that it shall operate continuously, that it shall be - compatible with the Licensee's own equipment and its software - configuration, nor that it shall meet the Licensee's requirements. - . - 9.4. The Licensor does not either expressly or tacitly warrant that the - Software does not infringe any or all third party intellectual right - relating to a patent, software or to any or all other property right. - Moreover, the Licensor shall not hold the Licensee harmless against 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 upon on a case-by-case - basis between the relevant Licensor and the Licensee pursuant to a - memorandum of understanding. The Licensor disclaims any or all liability as - regards the Licensee's use of the Software's name. No warranty shall be - provided as regards the existence of prior rights over the name of the - Software and 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. The Licensee whose Agreement is terminated shall no longer be - authorized to use, modify or distribute the Software. However, any or all - 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 PROVISIONS - -------------------------------------- - . - . - 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, notably, defective functioning, or - interruptions affecting the electricity or telecommunications networks, - blocking of the network following a virus attack, the intervention of the - government authorities, natural disasters, water damage, earthquakes, fire, - explosions, strikes and labor unrest, war, etc. - . - 11.2. The fact that either Party may fail, on one or several occasions, to - invoke one or several of the provisions hereof, shall under no - circumstances be interpreted as being a waiver by the interested Party of - its entitlement to invoke said provision(s) subsequently. - . - 11.3. The Agreement cancels and replaces any or all previous agreement, - 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 regards the Parties unless it is - made in writing and signed by their duly authorized representatives. - . - 11.4. In the event that one or several of the provisions hereof were to - conflict with a current or future applicable act or legislative text, said - act or legislative text shall take precedence, and the Parties shall make - the necessary amendments so as to be in compliance with said act or - legislative text. All the other provisions shall remain effective. - Similarly, the fact that a provision of the Agreement may be null and - void, for any reason whatsoever, shall not cause the Agreement as a whole - to be null and void. - . - 11.5. LANGUAGE - . - The Agreement is drafted in both French and English. In the event of a - conflict as regards construction, the French version shall be deemed - authentic. - . - . - Article 12 - NEW VERSIONS OF THE AGREEMENT - ------------------------------------------- - . - . - 12.1. Any or all 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, that 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 or all 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 settle the disagreements or disputes that may arise during the - performance of the Agreement out-of-court. - . - 13.2. In the absence of an out-of-court settlement 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 first Party to take action. - . - . - - -Files: maps/read_coherence_mapsembler/libchash.* - kissreads_g/read_coherence_mapsembler/libchash.* -Copyright: 1998-2005 Google Inc. -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 Google Inc. 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: minia/* -Copyright: 2012 Rayan Chiki <[email protected]> - 2012 Guillaume Rizk -License: CeCILL - -Files: * -Copyright: 2013 INRIA / IRISA -License: CeCILL - -Files: debian/* -Copyright: 2013 Olivier Sallou <[email protected]> -License: GPLv2+ - The Debian packaging is licensed under the GPL which is available at - `/usr/share/common-licenses/GPL'. - Copied: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/copyright (from rev 17772, trunk/packages/mapsembler2/trunk/debian/copyright) =================================================================== --- trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/copyright (rev 0) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/copyright 2014-08-19 06:53:11 UTC (rev 17782) @@ -0,0 +1,117 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: mapsembler2 +Source: http://colibread.inria.fr/mapsembler2 +Files-Excluded: + visu + results_visualization + mapsembler2_extremities/thirdparty/gatb-core/thirdparty/boost + mapsembler2_extremities/thirdparty/gatb-core/thirdparty/hdf5 + mapsembler2_extremities/thirdparty/gatb-core/doc/design + +Files: mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/* +Copyright: 2013 Giuseppe Ottaviano <[email protected]> +License: Apache v2.0 + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + . + http://www.apache.org/licenses/LICENSE-2.0 + . + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + +Files: kissreads_graph/read_coherence_mapsembler/libchash.* +Copyright: 1998-2005 Google Inc. +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 Google Inc. 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: minia/* +Copyright: 2012 Rayan Chiki <[email protected]> + 2012 Guillaume Rizk +License: AGPL-3+ + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + . + This program 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 Affero General Public License for more details. + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + . + The complete text of the GNU Affero General Public License + can be found in the file `/usr/share/doc/mapsembler2/LICENCE.md.gz'. + + +Files: mapsembler2_extremities/thirdparty/gatb-core/* +Copyright: 2014 INRIA R.Chikhi, G.Rizk, E.Drezen +License: AGPL-3+ + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + . + This program 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 Affero General Public License for more details. + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + . + The complete text of the GNU Affero General Public License + can be found in the file `/usr/share/doc/mapsembler2/LICENCE.md.gz'. + +Files: * +Copyright: 2013 INRIA / IRISA +License: AGPL-3+ + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + . + This program 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 Affero General Public License for more details. + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + . + The complete text of the GNU Affero General Public License + can be found in the file `/usr/share/doc/mapsembler2/LICENCE.md.gz'. + +Files: debian/* +Copyright: 2013 Olivier Sallou <[email protected]> +License: GPLv2+ + The Debian packaging is licensed under the GPL which is available at + `/usr/share/common-licenses/GPL'. + Deleted: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/docs =================================================================== Copied: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/docs (from rev 17770, trunk/packages/mapsembler2/trunk/debian/docs) =================================================================== Deleted: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.install =================================================================== --- trunk/packages/mapsembler2/trunk/debian/mapsembler2.install 2014-08-18 13:32:39 UTC (rev 17763) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.install 2014-08-19 06:53:11 UTC (rev 17782) @@ -1,2 +0,0 @@ -maps/mapsembler usr/bin/ -sample_example usr/share/doc/mapsembler2/ Copied: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.install (from rev 17766, trunk/packages/mapsembler2/trunk/debian/mapsembler2.install) =================================================================== --- trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.install (rev 0) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.install 2014-08-19 06:53:11 UTC (rev 17782) @@ -0,0 +1,6 @@ +#maps/mapsembler usr/bin/ +mapsembler2_extremities/build/mapsembler2_extremities usr/bin/ +mapsembler2_extend/mapsembler_extend usr/bin/ +#sample_example usr/share/doc/mapsembler2/ +kissreads_graph/kissreads_graph usr/bin/ +kissreads/kissreads usr/bin/ Deleted: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.manpages =================================================================== --- trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages 2014-08-18 13:32:39 UTC (rev 17763) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.manpages 2014-08-19 06:53:11 UTC (rev 17782) @@ -1 +0,0 @@ -mapsembler.1 Copied: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.manpages (from rev 17770, trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages) =================================================================== --- trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.manpages (rev 0) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/mapsembler2.manpages 2014-08-19 06:53:11 UTC (rev 17782) @@ -0,0 +1,5 @@ +mapsembler2_extremities.1 +mapsembler_extend.1 +kissreads.1 +kissreads_graph.1 + Copied: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/add_hardening (from rev 17773, trunk/packages/mapsembler2/trunk/debian/patches/add_hardening) =================================================================== --- trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/add_hardening (rev 0) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/add_hardening 2014-08-19 06:53:11 UTC (rev 17782) @@ -0,0 +1,84 @@ +Subject: add Debian hardening flags +Description: add hardening +Author: Olivier Sallou <[email protected]> +Last-Updated: 2014-08-18 +Forwarded: no +Index: mapsembler2_pipeline/kissreads/Makefile +=================================================================== +--- mapsembler2_pipeline.orig/kissreads/Makefile ++++ mapsembler2_pipeline/kissreads/Makefile +@@ -20,10 +20,14 @@ CC =gcc + # optimized flags + + #CFLAGS=-Wall -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!§ +-CFLAGS= -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@! ++#CFLAGS= -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@! + CFLAGS+=$(MYFLAGS) + #LDFLAGS+=-Wall -lm -O3 -lz -DOMP -fopenmp#-fopenmp +-LDFLAGS+= -lm -O3 -lz -DOMP -fopenmp#-fopenmp ++#LDFLAGS+= -lm -O3 -lz -DOMP -fopenmp#-fopenmp ++ ++CPPFLAGS += $(shell dpkg-buildflags --get CPPFLAGS) ++CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -lz ++LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS) -lm -O3 -lz + + ## debug flags + +Index: mapsembler2_pipeline/kissreads_graph/makefile +=================================================================== +--- mapsembler2_pipeline.orig/kissreads_graph/makefile ++++ mapsembler2_pipeline/kissreads_graph/makefile +@@ -4,6 +4,9 @@ EXEC=kissreads_graph + #Loader.cpp CFLAGS= -g -lz -std=c++11 -DMINIA_IS_IN_PARENT_FOLDER + #Loader.cpp + CFLAGS= -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER ++CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS) ++CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER ++LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS) + #CFLAGS= -g -lz -DMINIA_IS_IN_PARENT_FOLDER + SRC=block_allocator.cpp DeBruijnGraph.cpp Fragment.cpp json.cpp read_coherence_mapsembler/libchash.cpp read_coherence_mapsembler/couple.cpp read_coherence_mapsembler/misc_tools.cpp read_coherence_mapsembler/read_groups.cpp read_coherence_mapsembler/consensus_common.cpp read_coherence_mapsembler/list.cpp read_coherence_mapsembler/read_coherence.cpp read_coherence_mapsembler/interface_libchash.cpp commons.cpp ../minia/Kmer.cpp ../minia/Bank.cpp Loader.cpp ReadMapper.cpp + OBJ= $(SRC:.cpp=.o) +@@ -48,7 +51,7 @@ endif + all: $(EXEC) + + kissreads_graph: $(OBJ) KissReadsGraph.cpp +- $(CC) -o $@ $^ $(CFLAGS) ++ $(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS) + + %.o: %.cpp %.h + $(CC) -lz -o $@ -c $< $(CFLAGS) +Index: mapsembler2_pipeline/mapsembler2_extend/makefile +=================================================================== +--- mapsembler2_pipeline.orig/mapsembler2_extend/makefile ++++ mapsembler2_pipeline/mapsembler2_extend/makefile +@@ -3,6 +3,9 @@ EXEC=mapsembler_extend + #CFLAGS= -O4 -lz --std=gnu++0x + #CFLAGS= -g -lz -DMINIA_IS_IN_PARENT_FOLDER + CFLAGS= -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER ++CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS) ++CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER ++LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS) + #CFLAGS= -g -lz --std=gnu++0x -DMINIA_IS_IN_PARENT_FOLDER + #CFLAGS= -g -lz -DMINIA_IS_IN_PARENT_FOLDER + SRC=../minia/Pool.cpp ../minia/Bank.cpp ../minia/Bloom.cpp ../minia/Hash16.cpp ../minia/Terminator.cpp ../minia/Kmer.cpp ../minia/Traversal.cpp ../minia/LinearCounter.cpp ../minia/Set.cpp ../minia/Utils.cpp ../minia/SortingCount.cpp ../minia/Debloom.cpp ../minia/OAHash.cpp commons.cpp IterativeExtensions.cpp Fragment_Bank.cpp Fragment.cpp GraphOutput.cpp +@@ -49,7 +52,7 @@ all: $(EXEC) + + mapsembler_extend: $(OBJ) $(OBJ2) mapsembler_extend.cpp + #mapsembler: $(OBJ) $(OBJ2) test.cpp +- $(CC) -o $@ $^ $(CFLAGS) ++ $(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS) + + %.o: %.cpp %.h + $(CC) -lz -o $@ -c $< $(CFLAGS) +Index: mapsembler2_pipeline/mapsembler2_extremities/CMakeLists.txt +=================================================================== +--- mapsembler2_pipeline.orig/mapsembler2_extremities/CMakeLists.txt ++++ mapsembler2_pipeline/mapsembler2_extremities/CMakeLists.txt +@@ -2,6 +2,7 @@ project(mapsembler2_extremities) + + cmake_minimum_required(VERSION 2.6) + ++ + ################################################################################ + # Define cmake modules directory + ################################################################################ Deleted: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/series =================================================================== --- trunk/packages/mapsembler2/trunk/debian/patches/series 2014-08-18 13:32:39 UTC (rev 17763) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/series 2014-08-19 06:53:11 UTC (rev 17782) @@ -1 +0,0 @@ -fix_makefile Copied: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/series (from rev 17770, trunk/packages/mapsembler2/trunk/debian/patches/series) =================================================================== --- trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/series (rev 0) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/series 2014-08-19 06:53:11 UTC (rev 17782) @@ -0,0 +1,2 @@ +use_debian_libs +add_hardening Copied: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/use_debian_libs (from rev 17770, trunk/packages/mapsembler2/trunk/debian/patches/use_debian_libs) =================================================================== --- trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/use_debian_libs (rev 0) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/patches/use_debian_libs 2014-08-19 06:53:11 UTC (rev 17782) @@ -0,0 +1,194 @@ +Subject: use HDF5 lib in Debian +Description: use Debian libs instead of embedded one +Author: Olivier Sallou <[email protected]> +Last-Updated: 2014-08-18 +Forwarded: no +Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt +=================================================================== +--- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt ++++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt +@@ -2,47 +2,6 @@ + # HDF5 GENERATION + ################################################################################ + +-SET (HDF5_ENABLE_THREADSAFE ON) +- +-########## MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED ########## +-SET (HDF5_BUILD_TOOLS ON CACHE BOOL "Build HDF5 Tools") +-#SET (CMAKE_EXE_LINKER_FLAGS "-lpthread -lz") +- +-SET (HDF5_EXTERNALLY_CONFIGURED ON) +- +-#SET (HDF5_INSTALL_BIN_DIR ${PROJECT_BINARY_DIR}/bin/${CMAKE_BUILD_TYPE}) +-#SET (HDF5_INSTALL_LIB_DIR ${PROJECT_BINARY_DIR}/lib/${CMAKE_BUILD_TYPE}) +-SET (HDF5_INSTALL_BIN_DIR bin) +-SET (HDF5_INSTALL_LIB_DIR lib) +- +-SET (HDF5_INSTALL_INCLUDE_DIR ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5) +-SET (HDF5_INSTALL_DATA_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE}) +-SET (HDF5_INSTALL_CMAKE_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE}) +- +-IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE) +- SET (HDF5_EXPORTED_TARGETS "gatb-hdf5") +-ENDIF() +- +-# We don't want warnings from HDF5 compilation +-set (COMPILE_DEFINITIONS "${COMPILE_DEFINITIONS} -w") +-add_definitions (${COMPILE_DEFINITIONS}) +- +-# add HDF5 generation +-ADD_SUBDIRECTORY (hdf5) +- +-# We add a custom target for copying header files. +-add_custom_target (hdf5_postbuild ALL) +- +-# We build the output directory +-add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E make_directory ${HDF5_INSTALL_INCLUDE_DIR}) +- +-# We define all the header files to be copied +-file (GLOB headerfiles ${PROJECT_SOURCE_DIR}/thirdparty/hdf5/src/*.h ${PROJECT_BINARY_DIR}/thirdparty/hdf5/H5pubconf.h) +- +-# We copy each header file +-foreach (header ${headerfiles}) +- add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different ${header} ${HDF5_INSTALL_INCLUDE_DIR} ) +-endforeach() + + ################################################################################ + # EMPHF GENERATION +@@ -77,6 +36,5 @@ endforeach() + # INSTALL + ################################################################################ + IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE) +- INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5 DESTINATION include) + INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/emphf DESTINATION include) + ENDIF () +Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt +=================================================================== +--- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt ++++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt +@@ -173,7 +173,7 @@ ADD_SUBDIRECTORY(thirdparty) + # DEPENDENCIES + ################################################################################ + # we must be sure that hdf5 is built and installed before building gatb-core +-ADD_DEPENDENCIES (gatbcore-static hdf5 hdf5_postbuild emphf_copyasis) ++ADD_DEPENDENCIES (gatbcore-static hdf5 emphf_copyasis) + + + ################################################################################ +Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp +=================================================================== +--- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp ++++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp +@@ -35,7 +35,7 @@ + #include <stdint.h> + #include <algorithm> + #include <iostream> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + #include <gatb/system/api/Exception.hpp> + #include <gatb/tools/math/NativeInt64.hpp> +Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp +=================================================================== +--- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp ++++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp +@@ -40,7 +40,7 @@ + #include <string> + #include <vector> + #include <stdarg.h> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + /********************************************************************************/ + namespace gatb { +Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp +=================================================================== +--- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp ++++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp +@@ -32,7 +32,7 @@ + + #include <gatb/tools/storage/impl/CollectionHDF5.hpp> + #include <gatb/system/impl/System.hpp> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + #include <typeinfo> + + /********************************************************************************/ +Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp +=================================================================== +--- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp ++++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp +@@ -33,7 +33,7 @@ + /********************************************************************************/ + + #include <iostream> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + #include <gatb/system/api/types.hpp> + #include <gatb/tools/misc/api/Abundance.hpp> +Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt16.hpp +=================================================================== +--- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt16.hpp ++++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt16.hpp +@@ -31,7 +31,7 @@ + #include <iostream> + #include <gatb/system/api/types.hpp> + #include <gatb/tools/misc/api/Abundance.hpp> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + /********************************************************************************/ + namespace gatb { +Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp +=================================================================== +--- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp ++++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp +@@ -31,7 +31,7 @@ + #include <iostream> + #include <gatb/system/api/types.hpp> + #include <gatb/tools/misc/api/Abundance.hpp> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + extern const unsigned char revcomp_4NT[]; + extern const unsigned char comp_NT []; +Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp +=================================================================== +--- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp ++++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp +@@ -31,7 +31,7 @@ + #include <iostream> + #include <gatb/system/api/types.hpp> + #include <gatb/tools/misc/api/Abundance.hpp> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + /********************************************************************************/ + namespace gatb { +Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp +=================================================================== +--- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp ++++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp +@@ -27,7 +27,7 @@ + #define _GATB_CORE_TOOLS_MISC_IHISTOGRAM_HPP_ + + #include <gatb/system/api/ISmartPointer.hpp> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + /********************************************************************************/ + namespace gatb { +Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp +=================================================================== +--- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp ++++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp +@@ -31,7 +31,7 @@ + /********************************************************************************/ + + #include <sys/types.h> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + /********************************************************************************/ + namespace gatb { Deleted: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/rules =================================================================== --- trunk/packages/mapsembler2/trunk/debian/rules 2014-08-18 13:32:39 UTC (rev 17763) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/rules 2014-08-19 06:53:11 UTC (rev 17782) @@ -1,28 +0,0 @@ -#!/usr/bin/make -f - -# Uncomment this to turn on verbose mode. -#export DH_VERBOSE=1 - -SRC_VERSION =$(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p') - -%: - dh $@ - -get-orig-source: - uscan --verbose --force-download - -override_dh_auto_build: - dh_auto_build - cd maps && make - - -override_dh_clean: - cd maps && make clean - rm -f maps/mapsembler - rm -f mapsembler.1 - dh_clean - -override_dh_install: - help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./maps/mapsembler > mapsembler.1 - dh_install - Copied: trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/rules (from rev 17772, trunk/packages/mapsembler2/trunk/debian/rules) =================================================================== --- trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/rules (rev 0) +++ trunk/packages/mapsembler2/tags/2.2.1+dfsg-1/debian/rules 2014-08-19 06:53:11 UTC (rev 17782) @@ -0,0 +1,45 @@ +#!/usr/bin/make -f + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +SRC_VERSION =$(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p') + +CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) +CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) +CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) $(CPPFLAGS) +LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) + +%: + dh $@ + +get-orig-source: + uscan --verbose --force-download + +override_dh_auto_build: + mkdir mapsembler2_extremities/build + cd mapsembler2_extremities/build && cmake .. && make + cd mapsembler2_extend && make k=29 + cd kissreads_graph && make k=29 + cd kissreads && make k=29 + + +override_dh_clean: + rm -rf mapsembler2_extremities/build + cd mapsembler2_extend && make clean + cd kissreads_graph && make clean + cd kissreads && make clean + + rm -f mapsembler2_extremities.1 + rm -f mapsembler_extend.1 + rm -f kissreads.1 + rm -f kissreads_graph.1 + dh_clean + +override_dh_install: + help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./mapsembler2_extremities/build/mapsembler2_extremities > mapsembler2_extremities.1 + help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./mapsembler2_extend/mapsembler_extend > mapsembler_extend.1 + help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./kissreads/kissreads > kissreads.1 + help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./kissreads_graph/kissreads_graph > kissreads_graph.1 + dh_install + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
