[med-svn] r17782 - in trunk/packages/mapsembler2/tags: . 2.2.1+dfsg-1/debian 2.2.1+dfsg-1/debian/patches
Olivier Sallou
osallou at moszumanska.debian.org
Tue Aug 19 06:53:12 UTC 2014
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 <osallou at debian.org> Thu, 29 May 2014 15:07:28 +0200
-
-mapsembler2 (2.1.2+dfsg-1) unstable; urgency=low
-
- * New upstream release
-
- -- Olivier Sallou <osallou at debian.org> Fri, 21 Feb 2014 15:42:22 +0100
-
-mapsembler2 (2.0.31-1) unstable; urgency=low
-
- * New upstream release
-
- -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> Thu, 06 Feb 2014 08:06:55 +0100
-
-mapsembler2 (2.0.5+dfsg-1) unstable; urgency=medium
-
- * First debian package (Closes: #737099).
-
- -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> Thu, 29 May 2014 15:07:28 +0200
+
+mapsembler2 (2.1.2+dfsg-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 21 Feb 2014 15:42:22 +0100
+
+mapsembler2 (2.0.31-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> Thu, 06 Feb 2014 08:06:55 +0100
+
+mapsembler2 (2.0.5+dfsg-1) unstable; urgency=medium
+
+ * First debian package (Closes: #737099).
+
+ -- Olivier Sallou <osallou at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Olivier Sallou <osallou at debian.org>
-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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+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
-
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- 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 <rayan.chikhi at ens-cachan.org>
- 2012 Guillaume Rizk
-License: CeCILL
-
-Files: *
-Copyright: 2013 INRIA / IRISA
-License: CeCILL
-
-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'.
-
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 <giuott at gmail.com>
+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 <rayan.chikhi at ens-cachan.org>
+ 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 <osallou at debian.org>
+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 <osallou at debian.org>
+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 <osallou at debian.org>
+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
+
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