[med-svn] [populations] 02/13: Import Debian changes 1.2.32-2
Andreas Tille
tille at debian.org
Sat Nov 18 21:01:24 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository populations.
commit c1f38ef392634364bc1956beaacc5b17dfefc565
Author: Georges Khaznadar <georgesk at ofset.org>
Date: Thu Jun 30 22:35:36 2011 +0200
Import Debian changes 1.2.32-2
populations (1.2.32-2) unstable; urgency=low
* modified copyright data for html/libcss/* and html/libjs/*, thanks to
Luca Falavigna.
* uploaded to NEW. (Closes: #631020)
populations (1.2.32-1) unstable; urgency=low
* Initial release (Closes: #631020)
* Modified debian control files. Older ones are in the subdirectory
debian.orig/
* Created a manpage from existing documents.
* Added build-dependencies: qt4-qmake, libqt4-dev,
libfontconfig1-dev, libfreetype6-dev, libglib2.0-dev, libice-dev,
libpng12-dev, libsm-dev, libx11-dev, libxext-dev, libxrender-dev,
zlib1g-dev, g++-4.5
.
N.B.: the build-dependency on g++-4.5 is necessary because of a source
which cannot be compiled with g++-4.6
---
debian/README.source | 10 +
debian/changelog | 23 ++
debian/compat | 1 +
debian/control | 19 ++
debian/copyright | 523 +++++++++++++++++++++++++++++++++
debian/manpage.xml | 177 +++++++++++
debian/patches/debian-changes-1.2.32-1 | 104 +++++++
debian/patches/series | 1 +
debian/populations.1 | 204 +++++++++++++
debian/populations.manpages | 1 +
debian/rules | 13 +
debian/source/format | 1 +
12 files changed, 1077 insertions(+)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..4a617e6
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,10 @@
+populations for Debian
+----------------------
+
+This package was downloaded from
+http://ppa.launchpad.net/olivier-langella/ppa/ubuntu/pool/main/p/populations/populations_1.2.32-2~maverick1.tar.gz
+and the debian subdirectory was moved to debian.orig before compressing the
+orig.tar.gz file.
+
+
+ -- Georges Khaznadar <georgesk at ofset.org>, Sun, 19 Jun 2011 19:32:59 +0200
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..ce1425e
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,23 @@
+populations (1.2.32-2) unstable; urgency=low
+
+ * modified copyright data for html/libcss/* and html/libjs/*, thanks to
+ Luca Falavigna.
+ * uploaded to NEW. (Closes: #631020)
+
+ -- Georges Khaznadar <georgesk at ofset.org> Thu, 30 Jun 2011 22:35:36 +0200
+
+populations (1.2.32-1) unstable; urgency=low
+
+ * Initial release (Closes: #631020)
+ * Modified debian control files. Older ones are in the subdirectory
+ debian.orig/
+ * Created a manpage from existing documents.
+ * Added build-dependencies: qt4-qmake, libqt4-dev,
+ libfontconfig1-dev, libfreetype6-dev, libglib2.0-dev, libice-dev,
+ libpng12-dev, libsm-dev, libx11-dev, libxext-dev, libxrender-dev,
+ zlib1g-dev, g++-4.5
+ .
+ N.B.: the build-dependency on g++-4.5 is necessary because of a source
+ which cannot be compiled with g++-4.6
+
+ -- Georges Khaznadar <georgesk at ofset.org> Sun, 19 Jun 2011 22:31:51 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..7f8f011
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+7
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..2fb7ea3
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,19 @@
+Source: populations
+Section: science
+Priority: extra
+Maintainer: Georges Khaznadar <georgesk at ofset.org>
+Build-Depends: debhelper (>= 7.0.50~), cmake, qt4-qmake, libqt4-dev,
+ libfontconfig1-dev, libfreetype6-dev, libglib2.0-dev, libice-dev,
+ libpng12-dev, libsm-dev, libx11-dev, libxext-dev, libxrender-dev,
+ zlib1g-dev,
+ g++-4.5
+Standards-Version: 3.9.2
+Homepage: http://www.bioinformatics.org/~tryphon/populations/
+
+Package: populations
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, libqt4-xml (>= 4.5.2)
+Description: population genetic software
+ Populations is a population genetic software. It computes genetic
+ distances between populations or individuals. It builds phylogenetic
+ trees (NJ or UPGMA) with bootstrap values.
\ No newline at end of file
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..afcff0b
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,523 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: populations
+Source: http://ppa.launchpad.net/olivier-langella/ppa/ubuntu/pool/main/p/populations/populations_1.2.32-2~maverick1.tar.gz
+
+Files: *
+Copyright: 2005-2010 Olivier Langella <olivier.langella at laposte.net>
+License: GPL-2
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, version 2 of the License.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+Files: html/libcss/mathematica.css
+Copyright: 1999 The University Of Queensland
+Contributor: Roger B. Sidje <rbs at maths.uq.edu.au>License: MPL1.1
+License: MPL-1.1
+ see the complete text of the license below.
+
+Files: html/libjs/entity.js
+Copyright: 2002 The University of Queensland
+Contributor: Roger B. Sidje <rbs at maths.uq.edu.au>License: MPL1.1
+License: MPL-1.1
+ see the complete text of the license below.
+
+Files: html/libjs/viewmath.js
+Copyright: 2002 The University of Queensland
+Contributors: Roger B. Sidje <rbs at maths.uq.edu.au>
+ Steve Swanson <steve.swanson at mackichan.com>
+License: MPL-1.1
+ 1. Definitions.
+ .
+ 1.0.1. "Commercial Use" means distribution or otherwise making the
+ Covered Code available to a third party.
+ .
+ 1.1. "Contributor" means each entity that creates or contributes to
+ the creation of Modifications.
+ .
+ 1.2. "Contributor Version" means the combination of the Original
+ Code, prior Modifications used by a Contributor, and the Modifications
+ made by that particular Contributor.
+ .
+ 1.3. "Covered Code" means the Original Code or Modifications or the
+ combination of the Original Code and Modifications, in each case
+ including portions thereof.
+ .
+ 1.4. "Electronic Distribution Mechanism" means a mechanism generally
+ accepted in the software development community for the electronic
+ transfer of data.
+ .
+ 1.5. "Executable" means Covered Code in any form other than Source
+ Code.
+ .
+ 1.6. "Initial Developer" means the individual or entity identified
+ as the Initial Developer in the Source Code notice required by Exhibit
+ A.
+ .
+ 1.7. "Larger Work" means a work which combines Covered Code or
+ portions thereof with code not governed by the terms of this License.
+ .
+ 1.8. "License" means this document.
+ .
+ 1.8.1. "Licensable" means having the right to grant, to the maximum
+ extent possible, whether at the time of the initial grant or
+ subsequently acquired, any and all of the rights conveyed herein.
+ .
+ 1.9. "Modifications" means any addition to or deletion from the
+ substance or structure of either the Original Code or any previous
+ Modifications. When Covered Code is released as a series of files, a
+ Modification is:
+ A. Any addition to or deletion from the contents of a file
+ containing Original Code or previous Modifications.
+ .
+ B. Any new file that contains any part of the Original Code or
+ previous Modifications.
+ .
+ 1.10. "Original Code" means Source Code of computer software code
+ which is described in the Source Code notice required by Exhibit A as
+ Original Code, and which, at the time of its release under this
+ License is not already Covered Code governed by this License.
+ .
+ 1.10.1. "Patent Claims" means any patent claim(s), now owned or
+ hereafter acquired, including without limitation, method, process,
+ and apparatus claims, in any patent Licensable by grantor.
+ .
+ 1.11. "Source Code" means the preferred form of the Covered Code for
+ making modifications to it, including all modules it contains, plus
+ any associated interface definition files, scripts used to control
+ compilation and installation of an Executable, or source code
+ differential comparisons against either the Original Code or another
+ well known, available Covered Code of the Contributor's choice. The
+ Source Code can be in a compressed or archival form, provided the
+ appropriate decompression or de-archiving software is widely available
+ for no charge.
+ .
+ 1.12. "You" (or "Your") means an individual or a legal entity
+ exercising rights under, and complying with all of the terms of, this
+ License or a future version of this License issued under Section 6.1.
+ For legal entities, "You" includes any entity which controls, is
+ controlled by, or is under common control with You. For purposes of
+ this definition, "control" means (a) the power, direct or indirect,
+ to cause the direction or management of such entity, whether by
+ contract or otherwise, or (b) ownership of more than fifty percent
+ (50%) of the outstanding shares or beneficial ownership of such
+ entity.
+ .
+ 2. Source Code License.
+ .
+ 2.1. The Initial Developer Grant.
+ The Initial Developer hereby grants You a world-wide, royalty-free,
+ non-exclusive license, subject to third party intellectual property
+ claims:
+ (a) under intellectual property rights (other than patent or
+ trademark) Licensable by Initial Developer to use, reproduce,
+ modify, display, perform, sublicense and distribute the Original
+ Code (or portions thereof) with or without Modifications, and/or
+ as part of a Larger Work; and
+ .
+ (b) under Patents Claims infringed by the making, using or
+ selling of Original Code, to make, have made, use, practice,
+ sell, and offer for sale, and/or otherwise dispose of the
+ Original Code (or portions thereof).
+ .
+ (c) the licenses granted in this Section 2.1(a) and (b) are
+ effective on the date Initial Developer first distributes
+ Original Code under the terms of this License.
+ .
+ (d) Notwithstanding Section 2.1(b) above, no patent license is
+ granted: 1) for code that You delete from the Original Code; 2)
+ separate from the Original Code; or 3) for infringements caused
+ by: i) the modification of the Original Code or ii) the
+ combination of the Original Code with other software or devices.
+ .
+ 2.2. Contributor Grant.
+ Subject to third party intellectual property claims, each Contributor
+ hereby grants You a world-wide, royalty-free, non-exclusive license
+ .
+ (a) under intellectual property rights (other than patent or
+ trademark) Licensable by Contributor, to use, reproduce, modify,
+ display, perform, sublicense and distribute the Modifications
+ created by such Contributor (or portions thereof) either on an
+ unmodified basis, with other Modifications, as Covered Code
+ and/or as part of a Larger Work; and
+ .
+ (b) under Patent Claims infringed by the making, using, or
+ selling of Modifications made by that Contributor either alone
+ and/or in combination with its Contributor Version (or portions
+ of such combination), to make, use, sell, offer for sale, have
+ made, and/or otherwise dispose of: 1) Modifications made by that
+ Contributor (or portions thereof); and 2) the combination of
+ Modifications made by that Contributor with its Contributor
+ Version (or portions of such combination).
+ .
+ (c) the licenses granted in Sections 2.2(a) and 2.2(b) are
+ effective on the date Contributor first makes Commercial Use of
+ the Covered Code.
+ .
+ (d) Notwithstanding Section 2.2(b) above, no patent license is
+ granted: 1) for any code that Contributor has deleted from the
+ Contributor Version; 2) separate from the Contributor Version;
+ 3) for infringements caused by: i) third party modifications of
+ Contributor Version or ii) the combination of Modifications made
+ by that Contributor with other software (except as part of the
+ Contributor Version) or other devices; or 4) under Patent Claims
+ infringed by Covered Code in the absence of Modifications made by
+ that Contributor.
+ .
+ 3. Distribution Obligations.
+ .
+ 3.1. Application of License.
+ The Modifications which You create or to which You contribute are
+ governed by the terms of this License, including without limitation
+ Section 2.2. The Source Code version of Covered Code may be
+ distributed only under the terms of this License or a future version
+ of this License released under Section 6.1, and You must include a
+ copy of this License with every copy of the Source Code You
+ distribute. You may not offer or impose any terms on any Source Code
+ version that alters or restricts the applicable version of this
+ License or the recipients' rights hereunder. However, You may include
+ an additional document offering the additional rights described in
+ Section 3.5.
+ .
+ 3.2. Availability of Source Code.
+ Any Modification which You create or to which You contribute must be
+ made available in Source Code form under the terms of this License
+ either on the same media as an Executable version or via an accepted
+ Electronic Distribution Mechanism to anyone to whom you made an
+ Executable version available; and if made available via Electronic
+ Distribution Mechanism, must remain available for at least twelve (12)
+ months after the date it initially became available, or at least six
+ (6) months after a subsequent version of that particular Modification
+ has been made available to such recipients. You are responsible for
+ ensuring that the Source Code version remains available even if the
+ Electronic Distribution Mechanism is maintained by a third party.
+ .
+ 3.3. Description of Modifications.
+ You must cause all Covered Code to which You contribute to contain a
+ file documenting the changes You made to create that Covered Code and
+ the date of any change. You must include a prominent statement that
+ the Modification is derived, directly or indirectly, from Original
+ Code provided by the Initial Developer and including the name of the
+ Initial Developer in (a) the Source Code, and (b) in any notice in an
+ Executable version or related documentation in which You describe the
+ origin or ownership of the Covered Code.
+ .
+ 3.4. Intellectual Property Matters
+ (a) Third Party Claims.
+ If Contributor has knowledge that a license under a third party's
+ intellectual property rights is required to exercise the rights
+ granted by such Contributor under Sections 2.1 or 2.2,
+ Contributor must include a text file with the Source Code
+ distribution titled "LEGAL" which describes the claim and the
+ party making the claim in sufficient detail that a recipient will
+ know whom to contact. If Contributor obtains such knowledge after
+ the Modification is made available as described in Section 3.2,
+ Contributor shall promptly modify the LEGAL file in all copies
+ Contributor makes available thereafter and shall take other steps
+ (such as notifying appropriate mailing lists or newsgroups)
+ reasonably calculated to inform those who received the Covered
+ Code that new knowledge has been obtained.
+ .
+ (b) Contributor APIs.
+ If Contributor's Modifications include an application programming
+ interface and Contributor has knowledge of patent licenses which
+ are reasonably necessary to implement that API, Contributor must
+ also include this information in the LEGAL file.
+ .
+ (c) Representations.
+ Contributor represents that, except as disclosed pursuant to
+ Section 3.4(a) above, Contributor believes that Contributor's
+ Modifications are Contributor's original creation(s) and/or
+ Contributor has sufficient rights to grant the rights conveyed by
+ this License.
+ .
+ 3.5. Required Notices.
+ You must duplicate the notice in Exhibit A in each file of the Source
+ Code. If it is not possible to put such notice in a particular Source
+ Code file due to its structure, then You must include such notice in a
+ location (such as a relevant directory) where a user would be likely
+ to look for such a notice. If You created one or more Modification(s)
+ You may add your name as a Contributor to the notice described in
+ Exhibit A. You must also duplicate this License in any documentation
+ for the Source Code where You describe recipients' rights or ownership
+ rights relating to Covered Code. You may choose to offer, and to
+ charge a fee for, warranty, support, indemnity or liability
+ obligations to one or more recipients of Covered Code. However, You
+ may do so only on Your own behalf, and not on behalf of the Initial
+ Developer or any Contributor. You must make it absolutely clear than
+ any such warranty, support, indemnity or liability obligation is
+ offered by You alone, and You hereby agree to indemnify the Initial
+ Developer and every Contributor for any liability incurred by the
+ Initial Developer or such Contributor as a result of warranty,
+ support, indemnity or liability terms You offer.
+ .
+ 3.6. Distribution of Executable Versions.
+ You may distribute Covered Code in Executable form only if the
+ requirements of Section 3.1-3.5 have been met for that Covered Code,
+ and if You include a notice stating that the Source Code version of
+ the Covered Code is available under the terms of this License,
+ including a description of how and where You have fulfilled the
+ obligations of Section 3.2. The notice must be conspicuously included
+ in any notice in an Executable version, related documentation or
+ collateral in which You describe recipients' rights relating to the
+ Covered Code. You may distribute the Executable version of Covered
+ Code or ownership rights under a license of Your choice, which may
+ contain terms different from this License, provided that You are in
+ compliance with the terms of this License and that the license for the
+ Executable version does not attempt to limit or alter the recipient's
+ rights in the Source Code version from the rights set forth in this
+ License. If You distribute the Executable version under a different
+ license You must make it absolutely clear that any terms which differ
+ from this License are offered by You alone, not by the Initial
+ Developer or any Contributor. You hereby agree to indemnify the
+ Initial Developer and every Contributor for any liability incurred by
+ the Initial Developer or such Contributor as a result of any such
+ terms You offer.
+ .
+ 3.7. Larger Works.
+ You may create a Larger Work by combining Covered Code with other code
+ not governed by the terms of this License and distribute the Larger
+ Work as a single product. In such a case, You must make sure the
+ requirements of this License are fulfilled for the Covered Code.
+ .
+ 4. Inability to Comply Due to Statute or Regulation.
+ .
+ If it is impossible for You to comply with any of the terms of this
+ License with respect to some or all of the Covered Code due to
+ statute, judicial order, or regulation then You must: (a) comply with
+ the terms of this License to the maximum extent possible; and (b)
+ describe the limitations and the code they affect. Such description
+ must be included in the LEGAL file described in Section 3.4 and must
+ be included with all distributions of the Source Code. Except to the
+ extent prohibited by statute or regulation, such description must be
+ sufficiently detailed for a recipient of ordinary skill to be able to
+ understand it.
+ .
+ 5. Application of this License.
+ .
+ This License applies to code to which the Initial Developer has
+ attached the notice in Exhibit A and to related Covered Code.
+ .
+ 6. Versions of the License.
+ .
+ 6.1. New Versions.
+ Netscape Communications Corporation ("Netscape") may publish revised
+ and/or new versions of the License from time to time. Each version
+ will be given a distinguishing version number.
+ .
+ 6.2. Effect of New Versions.
+ Once Covered Code has been published under a particular version of the
+ License, You may always continue to use it under the terms of that
+ version. You may also choose to use such Covered Code under the terms
+ of any subsequent version of the License published by Netscape. No one
+ other than Netscape has the right to modify the terms applicable to
+ Covered Code created under this License.
+ .
+ 6.3. Derivative Works.
+ If You create or use a modified version of this License (which you may
+ only do in order to apply it to code which is not already Covered Code
+ governed by this License), You must (a) rename Your license so that
+ the phrases "Mozilla", "MOZILLAPL", "MOZPL", "Netscape",
+ "MPL", "NPL" or any confusingly similar phrase do not appear in your
+ license (except to note that your license differs from this License)
+ and (b) otherwise make it clear that Your version of the license
+ contains terms which differ from the Mozilla Public License and
+ Netscape Public License. (Filling in the name of the Initial
+ Developer, Original Code or Contributor in the notice described in
+ Exhibit A shall not of themselves be deemed to be modifications of
+ this License.)
+ .
+ 7. DISCLAIMER OF WARRANTY.
+ .
+ COVERED CODE IS PROVIDED UNDER THIS LICENSE ON AN "AS IS" BASIS,
+ WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
+ WITHOUT LIMITATION, WARRANTIES THAT THE COVERED CODE IS FREE OF
+ DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING.
+ THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE COVERED CODE
+ IS WITH YOU. SHOULD ANY COVERED CODE PROVE DEFECTIVE IN ANY RESPECT,
+ YOU (NOT THE INITIAL DEVELOPER OR ANY OTHER CONTRIBUTOR) ASSUME THE
+ COST OF ANY NECESSARY SERVICING, REPAIR OR CORRECTION. THIS DISCLAIMER
+ OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THIS LICENSE. NO USE OF
+ ANY COVERED CODE IS AUTHORIZED HEREUNDER EXCEPT UNDER THIS DISCLAIMER.
+ .
+ 8. TERMINATION.
+ .
+ 8.1. This License and the rights granted hereunder will terminate
+ automatically if You fail to comply with terms herein and fail to cure
+ such breach within 30 days of becoming aware of the breach. All
+ sublicenses to the Covered Code which are properly granted shall
+ survive any termination of this License. Provisions which, by their
+ nature, must remain in effect beyond the termination of this License
+ shall survive.
+ .
+ 8.2. If You initiate litigation by asserting a patent infringement
+ claim (excluding declatory judgment actions) against Initial Developer
+ or a Contributor (the Initial Developer or Contributor against whom
+ You file such action is referred to as "Participant") alleging that:
+ .
+ (a) such Participant's Contributor Version directly or indirectly
+ infringes any patent, then any and all rights granted by such
+ Participant to You under Sections 2.1 and/or 2.2 of this License
+ shall, upon 60 days notice from Participant terminate prospectively,
+ unless if within 60 days after receipt of notice You either: (i)
+ agree in writing to pay Participant a mutually agreeable reasonable
+ royalty for Your past and future use of Modifications made by such
+ Participant, or (ii) withdraw Your litigation claim with respect to
+ the Contributor Version against such Participant. If within 60 days
+ of notice, a reasonable royalty and payment arrangement are not
+ mutually agreed upon in writing by the parties or the litigation claim
+ is not withdrawn, the rights granted by Participant to You under
+ Sections 2.1 and/or 2.2 automatically terminate at the expiration of
+ the 60 day notice period specified above.
+ .
+ (b) any software, hardware, or device, other than such Participant's
+ Contributor Version, directly or indirectly infringes any patent, then
+ any rights granted to You by such Participant under Sections 2.1(b)
+ and 2.2(b) are revoked effective as of the date You first made, used,
+ sold, distributed, or had made, Modifications made by that
+ Participant.
+ .
+ 8.3. If You assert a patent infringement claim against Participant
+ alleging that such Participant's Contributor Version directly or
+ indirectly infringes any patent where such claim is resolved (such as
+ by license or settlement) prior to the initiation of patent
+ infringement litigation, then the reasonable value of the licenses
+ granted by such Participant under Sections 2.1 or 2.2 shall be taken
+ into account in determining the amount or value of any payment or
+ license.
+ .
+ 8.4. In the event of termination under Sections 8.1 or 8.2 above,
+ all end user license agreements (excluding distributors and resellers)
+ which have been validly granted by You or any distributor hereunder
+ prior to termination shall survive termination.
+ .
+ 9. LIMITATION OF LIABILITY.
+ .
+ UNDER NO CIRCUMSTANCES AND UNDER NO LEGAL THEORY, WHETHER TORT
+ (INCLUDING NEGLIGENCE), CONTRACT, OR OTHERWISE, SHALL YOU, THE INITIAL
+ DEVELOPER, ANY OTHER CONTRIBUTOR, OR ANY DISTRIBUTOR OF COVERED CODE,
+ OR ANY SUPPLIER OF ANY OF SUCH PARTIES, BE LIABLE TO ANY PERSON FOR
+ ANY INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES OF ANY
+ CHARACTER INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL,
+ WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER
+ COMMERCIAL DAMAGES OR LOSSES, EVEN IF SUCH PARTY SHALL HAVE BEEN
+ INFORMED OF THE POSSIBILITY OF SUCH DAMAGES. THIS LIMITATION OF
+ LIABILITY SHALL NOT APPLY TO LIABILITY FOR DEATH OR PERSONAL INJURY
+ RESULTING FROM SUCH PARTY'S NEGLIGENCE TO THE EXTENT APPLICABLE LAW
+ PROHIBITS SUCH LIMITATION. SOME JURISDICTIONS DO NOT ALLOW THE
+ EXCLUSION OR LIMITATION OF INCIDENTAL OR CONSEQUENTIAL DAMAGES, SO
+ THIS EXCLUSION AND LIMITATION MAY NOT APPLY TO YOU.
+ .
+ 10. U.S. GOVERNMENT END USERS.
+ .
+ The Covered Code is a "commercial item," as that term is defined in
+ 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer
+ software" and "commercial computer software documentation," as such
+ terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48
+ C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995),
+ all U.S. Government End Users acquire Covered Code with only those
+ rights set forth herein.
+ .
+ 11. MISCELLANEOUS.
+ .
+ This License represents the complete agreement concerning subject
+ matter hereof. If any provision of this License is held to be
+ unenforceable, such provision shall be reformed only to the extent
+ necessary to make it enforceable. This License shall be governed by
+ California law provisions (except to the extent applicable law, if
+ any, provides otherwise), excluding its conflict-of-law provisions.
+ With respect to disputes in which at least one party is a citizen of,
+ or an entity chartered or registered to do business in the United
+ States of America, any litigation relating to this License shall be
+ subject to the jurisdiction of the Federal Courts of the Northern
+ District of California, with venue lying in Santa Clara County,
+ California, with the losing party responsible for costs, including
+ without limitation, court costs and reasonable attorneys' fees and
+ expenses. The application of the United Nations Convention on
+ Contracts for the International Sale of Goods is expressly excluded.
+ Any law or regulation which provides that the language of a contract
+ shall be construed against the drafter shall not apply to this
+ License.
+ .
+ 12. RESPONSIBILITY FOR CLAIMS.
+ .
+ As between Initial Developer and the Contributors, each party is
+ responsible for claims and damages arising, directly or indirectly,
+ out of its utilization of rights under this License and You agree to
+ work with Initial Developer and Contributors to distribute such
+ responsibility on an equitable basis. Nothing herein is intended or
+ shall be deemed to constitute any admission of liability.
+ .
+13. MULTIPLE-LICENSED CODE.
+ .
+ Initial Developer may designate portions of the Covered Code as
+ "Multiple-Licensed". "Multiple-Licensed" means that the Initial
+ Developer permits you to utilize portions of the Covered Code under
+ Your choice of the NPL or the alternative licenses, if any, specified
+ by the Initial Developer in the file described in Exhibit A.
+ .
+ EXHIBIT A -Mozilla Public License.
+ .
+ ``The contents of this file are subject to the Mozilla Public License
+ Version 1.1 (the "License"); you may not use this file except in
+ compliance with the License. You may obtain a copy of the License at
+ http://www.mozilla.org/MPL/
+ .
+ Software distributed under the License is distributed on an "AS IS"
+ basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
+ License for the specific language governing rights and limitations
+ under the License.
+ .
+ The Original Code is ______________________________________.
+ .
+ The Initial Developer of the Original Code is ________________________.
+ Portions created by ______________________ are Copyright (C) ______
+ _______________________. All Rights Reserved.
+ .
+ Contributor(s): ______________________________________.
+ .
+ Alternatively, the contents of this file may be used under the terms
+ of the _____ license (the "[___] License"), in which case the
+ provisions of [______] License are applicable instead of those
+ above. If you wish to allow use of your version of this file only
+ under the terms of the [____] License and not to allow others to use
+ your version of this file under the MPL, indicate your decision by
+ deleting the provisions above and replace them with the notice and
+ other provisions required by the [___] License. If you do not delete
+ the provisions above, a recipient may use your version of this file
+ under either the MPL or the [___] License."
+ .
+ [NOTE: The text of this Exhibit A may differ slightly from the text of
+ the notices in the Source Code files of the Original Code. You should
+ use the text of this Exhibit A rather than the text found in the
+ Original Code Source Code for Your Modifications.]
+
+Files: debian/*
+Copyright: 2011 Georges Khaznadar <georgesk at ofset.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
diff --git a/debian/manpage.xml b/debian/manpage.xml
new file mode 100644
index 0000000..e6fba5a
--- /dev/null
+++ b/debian/manpage.xml
@@ -0,0 +1,177 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
+"http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
+
+<!--
+
+`xsltproc -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ /usr/share/xml/docbook/stylesheet/docbook-xsl/manpages/docbook.xsl \
+ manpage.xml'
+
+A manual page <package>.<section> will be generated. You may view the
+manual page with: nroff -man <package>.<section> | less'. A typical entry
+in a Makefile or Makefile.am is:
+
+DB2MAN = /usr/share/sgml/docbook/stylesheet/xsl/docbook-xsl/manpages/docbook.xsl
+XP = xsltproc -''-nonet -''-param man.charmap.use.subset "0"
+
+manpage.1: manpage.xml
+ $(XP) $(DB2MAN) $<
+
+The xsltproc binary is found in the xsltproc package. The XSL files are in
+docbook-xsl. A description of the parameters you can use can be found in the
+docbook-xsl-doc-* packages. Please remember that if you create the nroff
+version in one of the debian/rules file targets (such as build), you will need
+to include xsltproc and docbook-xsl in your Build-Depends control field.
+Alternatively use the xmlto command/package. That will also automatically
+pull in xsltproc and docbook-xsl.
+
+Notes for using docbook2x: docbook2x-man does not automatically create the
+AUTHOR(S) and COPYRIGHT sections. In this case, please add them manually as
+<refsect1> ... </refsect1>.
+
+To disable the automatic creation of the AUTHOR(S) and COPYRIGHT sections
+read /usr/share/doc/docbook-xsl/doc/manpages/authors.html. This file can be
+found in the docbook-xsl-doc-html package.
+
+Validation can be done using: `xmllint -''-noout -''-valid manpage.xml`
+
+General documentation about man-pages and man-page-formatting:
+man(1), man(7), http://www.tldp.org/HOWTO/Man-Page/
+
+-->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "Georges">
+ <!ENTITY dhsurname "Khaznadar">
+ <!-- dhusername could also be set to "&dhfirstname; &dhsurname;". -->
+ <!ENTITY dhusername "Georges Khaznadar">
+ <!ENTITY dhemail "georgesk at ofset.org">
+ <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+ allowed: see man(7), man(1) and
+ http://www.tldp.org/HOWTO/Man-Page/q2.html. -->
+ <!ENTITY dhsection "1">
+ <!-- TITLE should be something like "User commands" or similar (see
+ http://www.tldp.org/HOWTO/Man-Page/q2.html). -->
+ <!ENTITY dhtitle "populations User Manual">
+ <!ENTITY dhucpackage "POPULATIONS">
+ <!ENTITY dhpackage "populations">
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <authorgroup>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote this manpage for the Debian system.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <copyright>
+ <year>2011</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ <legalnotice>
+ <para>This manual page was written for the Debian system
+ (and may be used by others).</para>
+ <para>Permission is granted to copy, distribute and/or modify this
+ document under the terms of the GNU General Public License,
+ Version 2 or (at your option) any later version published by
+ the Free Software Foundation.</para>
+ <para>On Debian systems, the complete text of the GNU General Public
+ License can be found in
+ <filename>/usr/share/common-licenses/GPL</filename>.</para>
+ </legalnotice>
+ </refentryinfo>
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>population genetic software</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ </cmdsynopsis>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg><option><replaceable>name_of_input_file</replaceable></option></arg> <arg><option><replaceable>option</replaceable></option></arg> </cmdsynopsis>
+ <para>You can use <command>&dhpackage;</command> as a command line programm (very useful for batch treatment) to infer phylogenetic trees.</para>
+ </refsynopsisdiv>
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para><command>&dhpackage;</command> is a population genetic software. It computes genetic
+ distances between populations or individuals. It builds phylogenetic
+ trees (NJ or UPGMA) with bootstrap values.</para>
+ </refsect1>
+ <refsect1>
+ <title>Features</title>
+ <itemizedlist>
+ <listitem><para>haploids, diploids or polyploids genotypes (see input formats)</para></listitem>
+ <listitem><para>structured populations (see input files structured populations</para></listitem>
+ <listitem><para>No limit of populations, loci, alleles per loci (see input formats)</para></listitem>
+ <listitem><para>Distances between individuals (15 different methods)</para></listitem>
+ <listitem><para>Distances between populations (15 methods)</para></listitem>
+ <listitem><para>Bootstraps on loci OR individuals</para></listitem>
+ <listitem><para>Phylogenetic trees (individuals or populations), using Neighbor Joining or UPGMA (PHYLIP tree format)</para></listitem>
+ <listitem><para>Allelic diversity</para></listitem>
+ <listitem><para>Converts data files from Genepop to different formats (Genepop, Genetix, Msat, Populations...)</para></listitem>
+ </itemizedlist>
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+ <variablelist>
+ <varlistentry>
+ <term><option>-phylogeny</option> <replaceable>ind|pop</replaceable></term>
+ <listitem><para>(default) for phylogenetic trees based on individuals or populations
+ </para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>dist</option> <replaceable>method</replaceable></term>
+ <listitem><para>(default: Nei standard, Ds) you can choose among: DAS, Dm, Ds, Dc, Da, dmu2, Fst, Cp, Dr, ASD, Dsw, Dr, Dru, Drw, Drl. see distances for details.
+ </para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-construct</option> <replaceable>method</replaceable></term>
+ <listitem><para>(default: upgma) possibilities upgma or nj (Neighbor Joining)
+ </para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-bootstrap_ind</option> <replaceable>n</replaceable></term>
+ <listitem><para>number to indicate the number of bootstraps to perform on individuals
+ </para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-bootstrap_locus</option> <replaceable>n</replaceable></term>
+ <listitem><para>
+ </para></listitem>number to indicate the number of bootstraps to perform on loci
+ </varlistentry>
+ <varlistentry>
+ <term><option>-output</option> <replaceable>name_of_treeview_file</replaceable></term>
+ <listitem><para>to indicate the name of the tree file (phylip tree format)
+ </para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-level</option> <replaceable>n</replaceable></term>
+ <listitem><para>number , structured populations allows to choose the structuration factor (in the example: town level is 1, building level is 2...).
+ </para></listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1>
+ <title>EXAMPLE</title>
+ <para><command>populations toutc2.txt -phylogeny pop -dist Dm -bootstrap_locus 10000 -output toutc2_10000_Dm.tre</command></para>
+ <para>Commands can be write in a .bat file (for DOS) or a script file (for UNIX)</para>
+ </refsect1>
+</refentry>
+
diff --git a/debian/patches/debian-changes-1.2.32-1 b/debian/patches/debian-changes-1.2.32-1
new file mode 100644
index 0000000..853ef58
--- /dev/null
+++ b/debian/patches/debian-changes-1.2.32-1
@@ -0,0 +1,104 @@
+Description: Upstream changes introduced in version 1.2.32-1
+ This patch has been created by dpkg-source during the package build.
+ Here's the last changelog entry, hopefully it gives details on why
+ those changes were made:
+ .
+ populations (1.2.32-1) unstable; urgency=low
+ .
+ * Initial release (Closes: #631020)
+ * Modified debian control files. Older ones are in the subdirectory
+ debian.orig/
+ * Created a manpage from existing documents.
+ * Added build-dependencies: qt4-qmake, libqt4-dev,
+ libfontconfig1-dev, libfreetype6-dev, libglib2.0-dev, libice-dev,
+ libpng12-dev, libsm-dev, libx11-dev, libxext-dev, libxrender-dev,
+ zlib1g-dev, g++-4.5
+ .
+ N.B.: the build-dependency on g++-4.5 is necessary because of a source
+ which cannot be compiled with g++-4.6
+ .
+ The person named in the Author field signed this changelog entry.
+Author: Georges Khaznadar <georgesk at ofset.org>
+Bug-Debian: http://bugs.debian.org/631020
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+--- /dev/null
++++ populations-1.2.32/TODO
+@@ -0,0 +1,65 @@
++Note :
++ il y a un échec à la construction avec pbuilder que je ne m'explique
++ pas ! avec debuild la compilation se passe bien, mais avec pbuilder
++ la ligature ne se fait pas bien :
++
++avec debuild :
++/usr/bin/c++ -g -O2 -O3 -DNDEBUG
++ CMakeFiles/populations.dir/populations.cpp.o
++ CMakeFiles/populations.dir/distgnt.cpp.o
++ CMakeFiles/populations.dir/jeupopexp.cpp.o
++ CMakeFiles/populations.dir/fstat.cpp.o
++ CMakeFiles/populations.dir/jeupop.cpp.o
++ CMakeFiles/populations.dir/applpop.cpp.o
++ CMakeFiles/populations.dir/applpopulations.cpp.o
++ CMakeFiles/populations.dir/matrices.cpp.o
++ CMakeFiles/populations.dir/applications.cpp.o
++ CMakeFiles/populations.dir/arbre.cpp.o
++ CMakeFiles/populations.dir/arbreplus.cpp.o
++ CMakeFiles/populations.dir/couleur.cpp.o
++ CMakeFiles/populations.dir/vecteurs.cpp.o
++ CMakeFiles/populations.dir/locus.cpp.o
++ CMakeFiles/populations.dir/allele.cpp.o
++ CMakeFiles/populations.dir/individu.cpp.o
++ CMakeFiles/populations.dir/strucpop.cpp.o
++ CMakeFiles/populations.dir/chaineficpop.cpp.o
++ CMakeFiles/populations.dir/metapop.cpp.o
++ CMakeFiles/populations.dir/population.cpp.o -o populations
++ -rdynamic -lQtGui -lpng -lSM -lICE -lXrender -lfreetype
++ -lfontconfig -lXext -lX11 -lm -lQtXml -lQtCore -lz -lgthread-2.0
++ -lglib-2.0 -lgobject-2.0 -lrt -lpthread -ldl -lm
++
++et ça réussit.
++
++avec pbuilder :
++/usr/bin/c++ -g -O2 -O3 -DNDEBUG
++ CMakeFiles/populations.dir/populations.cpp.o
++ CMakeFiles/populations.dir/distgnt.cpp.o
++ CMakeFiles/populations.dir/jeupopexp.cpp.o
++ CMakeFiles/populations.dir/fstat.cpp.o
++ CMakeFiles/populations.dir/jeupop.cpp.o
++ CMakeFiles/populations.dir/applpop.cpp.o
++ CMakeFiles/populations.dir/applpopulations.cpp.o
++ CMakeFiles/populations.dir/matrices.cpp.o
++ CMakeFiles/populations.dir/applications.cpp.o
++ CMakeFiles/populations.dir/arbre.cpp.o
++ CMakeFiles/populations.dir/arbreplus.cpp.o
++ CMakeFiles/populations.dir/couleur.cpp.o
++ CMakeFiles/populations.dir/vecteurs.cpp.o
++ CMakeFiles/populations.dir/locus.cpp.o
++ CMakeFiles/populations.dir/allele.cpp.o
++ CMakeFiles/populations.dir/individu.cpp.o
++ CMakeFiles/populations.dir/strucpop.cpp.o
++ CMakeFiles/populations.dir/chaineficpop.cpp.o
++ CMakeFiles/populations.dir/metapop.cpp.o
++ CMakeFiles/populations.dir/population.cpp.o -o populations
++ -rdynamic -lQtGui -lQtXml -lQtCore -lm
++
++et ça échoue avec un message :
++CMakeFiles/populations.dir/arbre.cpp.o: In function `MatriceF':
++/tmp/populations-1.2.32/src/matrices.h:312: undefined reference to `biolib::vecteurs::Matrice<float>::Matrice(unsigned long, unsigned long)'
++
++
++Déjà pour commencer, il semble que le script configure ne donne pas le
++ même résultat, va savoir pourquoi : en effet, la liste des
++ bibliothèques liées n'est pas la même dans les deux cas.
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..b6e5e34
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+debian-changes-1.2.32-1
diff --git a/debian/populations.1 b/debian/populations.1
new file mode 100644
index 0000000..620d073
--- /dev/null
+++ b/debian/populations.1
@@ -0,0 +1,204 @@
+'\" t
+.\" Title: POPULATIONS
+.\" Author: Georges Khaznadar <georgesk at ofset.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/19/2011
+.\" Manual: populations User Manual
+.\" Source: populations
+.\" Language: English
+.\"
+.TH "POPULATIONS" "1" "06/19/2011" "populations" "populations User Manual"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+populations \- population genetic software
+.SH "SYNOPSIS"
+.HP \w'\fBpopulations\fR\ 'u
+\fBpopulations\fR
+.HP \w'\fBpopulations\fR\ 'u
+\fBpopulations\fR [\fB\fIname_of_input_file\fR\fR] [\fB\fIoption\fR\fR]
+.PP
+You can use
+\fBpopulations\fR
+as a command line programm (very useful for batch treatment) to infer phylogenetic trees\&.
+.SH "DESCRIPTION"
+.PP
+\fBpopulations\fR
+is a population genetic software\&. It computes genetic distances between populations or individuals\&. It builds phylogenetic trees (NJ or UPGMA) with bootstrap values\&.
+.SH "FEATURES"
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+haploids, diploids or polyploids genotypes (see input formats)
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+structured populations (see input files structured populations
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+No limit of populations, loci, alleles per loci (see input formats)
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Distances between individuals (15 different methods)
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Distances between populations (15 methods)
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Bootstraps on loci OR individuals
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Phylogenetic trees (individuals or populations), using Neighbor Joining or UPGMA (PHYLIP tree format)
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Allelic diversity
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Converts data files from Genepop to different formats (Genepop, Genetix, Msat, Populations\&.\&.\&.)
+.RE
+.SH "OPTIONS"
+.PP
+\fB\-phylogeny\fR \fIind|pop\fR
+.RS 4
+(default) for phylogenetic trees based on individuals or populations
+.RE
+.PP
+\fBdist\fR \fImethod\fR
+.RS 4
+(default: Nei standard, Ds) you can choose among: DAS, Dm, Ds, Dc, Da, dmu2, Fst, Cp, Dr, ASD, Dsw, Dr, Dru, Drw, Drl\&. see distances for details\&.
+.RE
+.PP
+\fB\-construct\fR \fImethod\fR
+.RS 4
+(default: upgma) possibilities upgma or nj (Neighbor Joining)
+.RE
+.PP
+\fB\-bootstrap_ind\fR \fIn\fR
+.RS 4
+number to indicate the number of bootstraps to perform on individuals
+.RE
+.PP
+\fB\-bootstrap_locus\fR \fIn\fR
+.RS 4
+
+number to indicate the number of bootstraps to perform on loci
+ .RE
+.PP
+\fB\-output\fR \fIname_of_treeview_file\fR
+.RS 4
+to indicate the name of the tree file (phylip tree format)
+.RE
+.PP
+\fB\-level\fR \fIn\fR
+.RS 4
+number , structured populations allows to choose the structuration factor (in the example: town level is 1, building level is 2\&.\&.\&.)\&.
+.RE
+.SH "EXAMPLE"
+.PP
+\fBpopulations toutc2\&.txt \-phylogeny pop \-dist Dm \-bootstrap_locus 10000 \-output toutc2_10000_Dm\&.tre\fR
+.PP
+Commands can be write in a \&.bat file (for DOS) or a script file (for UNIX)
+.SH "AUTHOR"
+.PP
+\fBGeorges Khaznadar\fR <\&georgesk at ofset\&.org\&>
+.RS 4
+Wrote this manpage for the Debian system\&.
+.RE
+.SH "COPYRIGHT"
+.br
+Copyright \(co 2011 Georges Khaznadar
+.br
+.PP
+This manual page was written for the Debian system (and may be used by others)\&.
+.PP
+Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or (at your option) any later version published by the Free Software Foundation\&.
+.PP
+On Debian systems, the complete text of the GNU General Public License can be found in
+/usr/share/common\-licenses/GPL\&.
+.sp
diff --git a/debian/populations.manpages b/debian/populations.manpages
new file mode 100644
index 0000000..4bac602
--- /dev/null
+++ b/debian/populations.manpages
@@ -0,0 +1 @@
+debian/populations.1
\ No newline at end of file
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..7678a50
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ export CC=gcc-4.5 CXX=g++-4.5; dh $@
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/populations.git
More information about the debian-med-commit
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