[med-svn] r15747 - in trunk/packages/minia/trunk: . debian debian/patches debian/source
Olivier Sallou
osallou at moszumanska.debian.org
Mon Jan 13 11:19:10 UTC 2014
Author: osallou
Date: 2014-01-13 11:19:10 +0000 (Mon, 13 Jan 2014)
New Revision: 15747
Added:
trunk/packages/minia/trunk/debian/
trunk/packages/minia/trunk/debian/README.debian
trunk/packages/minia/trunk/debian/changelog
trunk/packages/minia/trunk/debian/compat
trunk/packages/minia/trunk/debian/control
trunk/packages/minia/trunk/debian/copyright
trunk/packages/minia/trunk/debian/minia.install
trunk/packages/minia/trunk/debian/patches/
trunk/packages/minia/trunk/debian/patches/add_hardening
trunk/packages/minia/trunk/debian/patches/series
trunk/packages/minia/trunk/debian/rules
trunk/packages/minia/trunk/debian/source/
trunk/packages/minia/trunk/debian/source/format
trunk/packages/minia/trunk/debian/upstream
trunk/packages/minia/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications (1.6067+dfsg-1) to trunk
Property changes on: trunk/packages/minia/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/minia/trunk/debian/README.debian
===================================================================
--- trunk/packages/minia/trunk/debian/README.debian (rev 0)
+++ trunk/packages/minia/trunk/debian/README.debian 2014-01-13 11:19:10 UTC (rev 15747)
@@ -0,0 +1,8 @@
+minia for DEBIAN
+-------------------
+
+No man page is available but to get help, just type: ./minia
+
+Minia is not built with openmp support but it does not provide a *configure* like build mechanism to detect if openmp is supported (depending on archs, compiler etc..).
+
+ -- Olivier Sallou <osallou at debian.org> Mon, 13 Jan 2014 10:55:29 +0100
Added: trunk/packages/minia/trunk/debian/changelog
===================================================================
--- trunk/packages/minia/trunk/debian/changelog (rev 0)
+++ trunk/packages/minia/trunk/debian/changelog 2014-01-13 11:19:10 UTC (rev 15747)
@@ -0,0 +1,6 @@
+minia (1.6067+dfsg-1) UNRELEASED; urgency=medium
+
+ * First debian package (Closes: #735158).
+
+ -- Olivier Sallou <osallou at debian.org> Sat, 21 Dec 2013 16:55:29 +0100
+
Added: trunk/packages/minia/trunk/debian/compat
===================================================================
--- trunk/packages/minia/trunk/debian/compat (rev 0)
+++ trunk/packages/minia/trunk/debian/compat 2014-01-13 11:19:10 UTC (rev 15747)
@@ -0,0 +1 @@
+9
Added: trunk/packages/minia/trunk/debian/control
===================================================================
--- trunk/packages/minia/trunk/debian/control (rev 0)
+++ trunk/packages/minia/trunk/debian/control 2014-01-13 11:19:10 UTC (rev 15747)
@@ -0,0 +1,21 @@
+Source: minia
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/minia/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/minia/trunk/
+Homepage: http://minia.genouest.org/
+
+Package: minia
+Architecture: any
+Depends: ${misc:Depends}, ${shlibs:Depends}
+Description: short-read assembler
+ Short-read assembler based on a de Bruijn graph, capable of assembling a
+ human genome on a desktop computer in a day.
+ .
+ The output of Minia is a set of contigs.
+ Minia produces results of similar contiguity and accuracy to other
+ de Bruijn assemblers (e.g. Velvet).
Added: trunk/packages/minia/trunk/debian/copyright
===================================================================
--- trunk/packages/minia/trunk/debian/copyright (rev 0)
+++ trunk/packages/minia/trunk/debian/copyright 2014-01-13 11:19:10 UTC (rev 15747)
@@ -0,0 +1,511 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: minia
+Source: http://minia.genouest.org
+Files-Excluded:
+ manual/manual.pdf
+
+Files: *
+Copyright: 2012 Rayan Chiki <rayan.chikhi at ens-cachan.org>
+ 2012 Guillaume Rizk
+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.
+ .
+ .
+ Version 1.1 of 10/26/2004
+
+Files: debian/*
+Copyright: 2013 Olivier Sallou <osallou at debian.org>
+License: GPLv2+
+ The Debian packaging is licensed under the GPL which is available at
+ `/usr/share/common-licenses/GPL'.
+
Added: trunk/packages/minia/trunk/debian/minia.install
===================================================================
--- trunk/packages/minia/trunk/debian/minia.install (rev 0)
+++ trunk/packages/minia/trunk/debian/minia.install 2014-01-13 11:19:10 UTC (rev 15747)
@@ -0,0 +1 @@
+minia usr/bin/
Added: trunk/packages/minia/trunk/debian/patches/add_hardening
===================================================================
--- trunk/packages/minia/trunk/debian/patches/add_hardening (rev 0)
+++ trunk/packages/minia/trunk/debian/patches/add_hardening 2014-01-13 11:19:10 UTC (rev 15747)
@@ -0,0 +1,20 @@
+--- a/makefile
++++ b/makefile
+@@ -1,5 +1,7 @@
+ CC=g++
+-CFLAGS = -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
++CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
++LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
+ SRC=Pool.cpp Bank.cpp Bloom.cpp Hash16.cpp LargeInt.cpp Kmer.cpp Terminator.cpp Traversal.cpp LinearCounter.cpp Set.cpp Utils.cpp SortingCount.cpp Debloom.cpp OAHash.cpp
+ EXEC=minia
+ OBJ= $(SRC:.cpp=.o)
+@@ -60,7 +62,7 @@
+ all: $(EXEC)
+
+ minia: clean $(OBJ) Minia.cpp
+- $(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) -lz
++ $(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) $(LDFLAGS) -lz
+
+ %.o: %.cpp %.h
+ $(CC) -o $@ -c $< $(CFLAGS)
Added: trunk/packages/minia/trunk/debian/patches/series
===================================================================
--- trunk/packages/minia/trunk/debian/patches/series (rev 0)
+++ trunk/packages/minia/trunk/debian/patches/series 2014-01-13 11:19:10 UTC (rev 15747)
@@ -0,0 +1 @@
+add_hardening
Added: trunk/packages/minia/trunk/debian/rules
===================================================================
--- trunk/packages/minia/trunk/debian/rules (rev 0)
+++ trunk/packages/minia/trunk/debian/rules 2014-01-13 11:19:10 UTC (rev 15747)
@@ -0,0 +1,15 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+%:
+ dh $@
+
+get-orig-source:
+ uscan --verbose --force-download --repack --repack-compression xz
+
+override_dh_clean:
+ dh_clean
+ rm -f minia
Property changes on: trunk/packages/minia/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/minia/trunk/debian/source/format
===================================================================
--- trunk/packages/minia/trunk/debian/source/format (rev 0)
+++ trunk/packages/minia/trunk/debian/source/format 2014-01-13 11:19:10 UTC (rev 15747)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/minia/trunk/debian/upstream
===================================================================
--- trunk/packages/minia/trunk/debian/upstream (rev 0)
+++ trunk/packages/minia/trunk/debian/upstream 2014-01-13 11:19:10 UTC (rev 15747)
@@ -0,0 +1,11 @@
+Reference:
+ Author: Don Gilbert
+ Title: Sequence file format conversion with command-line readseq
+ Journal: Current Protocols in Bioinformatics
+ Year: 2003
+ Volume: Appendix 1
+ Pages: E
+ DOI: 10.1002/0471250953.bia01es00
+ PMID: 18428689
+ URL: http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bia01es00/abstract
+ eprint: http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bia01es00/pdf
Added: trunk/packages/minia/trunk/debian/watch
===================================================================
--- trunk/packages/minia/trunk/debian/watch (rev 0)
+++ trunk/packages/minia/trunk/debian/watch 2014-01-13 11:19:10 UTC (rev 15747)
@@ -0,0 +1,3 @@
+version=3
+
+opts="dversionmangle=s/\+dfsg//g" http://minia.genouest.org \./files/minia-([.\d]+)\.tar\.gz
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