[med-svn] r9172 - in trunk/packages/gassst/trunk: . debian debian/source

olivier sallou osallou-guest at alioth.debian.org
Wed Jan 4 15:20:59 UTC 2012


Author: osallou-guest
Date: 2012-01-04 15:20:59 +0000 (Wed, 04 Jan 2012)
New Revision: 9172

Added:
   trunk/packages/gassst/trunk/debian/
   trunk/packages/gassst/trunk/debian/changelog
   trunk/packages/gassst/trunk/debian/compat
   trunk/packages/gassst/trunk/debian/control
   trunk/packages/gassst/trunk/debian/copyright
   trunk/packages/gassst/trunk/debian/dirs
   trunk/packages/gassst/trunk/debian/docs
   trunk/packages/gassst/trunk/debian/gassst.1
   trunk/packages/gassst/trunk/debian/gassst.install
   trunk/packages/gassst/trunk/debian/gassst.manpages
   trunk/packages/gassst/trunk/debian/gassst_to_sam.1
   trunk/packages/gassst/trunk/debian/rules
   trunk/packages/gassst/trunk/debian/source/
   trunk/packages/gassst/trunk/debian/source/format
   trunk/packages/gassst/trunk/debian/upstream-metadata.yaml
   trunk/packages/gassst/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications (1.28-1) to trunk


Property changes on: trunk/packages/gassst/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Added: trunk/packages/gassst/trunk/debian/changelog
===================================================================
--- trunk/packages/gassst/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/changelog	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1,5 @@
+gassst (1.28-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #654603)
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr>  Wed, 04 Jan 2012 14:57:27 +0100

Added: trunk/packages/gassst/trunk/debian/compat
===================================================================
--- trunk/packages/gassst/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/compat	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1 @@
+8

Added: trunk/packages/gassst/trunk/debian/control
===================================================================
--- trunk/packages/gassst/trunk/debian/control	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/control	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1,19 @@
+Source: gassst
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <olivier.sallou at irisa.fr>
+DM-Upload-Allowed: yes
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/gassst/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gassst/trunk/
+Build-Depends: debhelper (>= 8.0.0)
+Standards-Version: 3.9.2
+Homepage: http://www.irisa.fr/symbiose/projects/gassst/
+
+Package: gassst
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Global alignment short sequence search tool
+ GASSST finds global alignments of short DNA sequences against large DNA banks.
+ Its strong point is its ability to perform fast gapped alignments.
+ The program takes as inputs banks in FASTA format and finds best alignment.

Added: trunk/packages/gassst/trunk/debian/copyright
===================================================================
--- trunk/packages/gassst/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/copyright	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1,518 @@
+Format: http://anonscm.debian.org/viewvc/dep/web/deps/dep5.mdwn?revision=174
+Upstream-Name: GASSST
+Source: http://www.irisa.fr/symbiose/projects/gassst/
+
+Files: debian/*
+Copyright: 2011 Olivier Sallou <olivier.sallou at irisa.fr>
+License: GPL-3
+ On Debian systems, the full text of the GNU General Public
+ License version 3 can be found in the file
+ `/usr/share/common-licenses/GPL-3'.
+
+Files: *
+Copyright: 2011, IRISA Guillaume Rizk <Guillaume.Rizk at irisa.fr>
+           2011, IRISA Dominique Lavanier <Dominique.lavenier at irisa.fr>
+License: CeCILL
+ Notice
+ .
+ This Agreement is a Free Software license agreement that is the result
+ of discussions between its authors in order to ensure compliance with
+ the two main principles guiding its drafting:
+ .
+     * firstly, compliance with the principles governing the distribution
+       of Free Software: access to source code, broad rights granted to
+       users,
+     * secondly, the election of a governing law, French law, with which
+       it is conformant, both as regards the law of torts and
+       intellectual property law, and the protection that it offers to
+       both authors and holders of the economic rights over software.
+ .
+ The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+ license are:
+ .
+ Commissariat à l'Energie Atomique - CEA, a public scientific, technical
+ and industrial research establishment, having its principal place of
+ business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
+ .
+ Centre National de la Recherche Scientifique - CNRS, a public scientific
+ and technological establishment, having its principal place of business
+ at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
+ .
+ Institut National de Recherche en Informatique et en Automatique -
+ INRIA, a public scientific and technological establishment, having its
+ principal place of business at Domaine de Voluceau, Rocquencourt, BP
+ 105, 78153 Le Chesnay cedex, France.
+ .
+ .
+     Preamble
+ .
+ The purpose of this Free Software license agreement is to grant users
+ the right to modify and redistribute the software governed by this
+ license within the framework of an open source distribution model.
+ .
+ The exercising of these rights is conditional upon certain obligations
+ for users so as to preserve this status for all subsequent redistributions.
+ .
+ In consideration of access to the source code and the rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors only have limited liability.
+ .
+ In this respect, the risks associated with loading, using, modifying
+ and/or developing or reproducing the software by the user are brought to
+ the user's attention, given its Free Software status, which may make it
+ complicated to use, with the result that its use is reserved for
+ developers and experienced professionals having in-depth computer
+ knowledge. Users are therefore encouraged to load and test the
+ suitability of the software as regards their requirements in conditions
+ enabling the security of their systems and/or data to be ensured and,
+ more generally, to use and operate it in the same conditions of
+ security. This Agreement may be freely reproduced and published,
+ provided it is not altered, and that no provisions are either added or
+ removed herefrom.
+ .
+ This Agreement may apply to any or all software for which the holder of
+ the economic rights decides to submit the use thereof to its provisions.
+ .
+ .
+     Article 1 - DEFINITIONS
+ .
+ For the purpose of this Agreement, when the following expressions
+ commence with a capital letter, they shall have the following meaning:
+ .
+ Agreement: means this license agreement, and its possible subsequent
+ versions and annexes.
+ .
+ Software: means the software in its Object Code and/or Source Code form
+ and, where applicable, its documentation, "as is" when the Licensee
+ accepts the Agreement.
+ .
+ Initial Software: means the Software in its Source Code and possibly its
+ Object Code form and, where applicable, its documentation, "as is" when
+ it is first distributed under the terms and conditions of the Agreement.
+ .
+ Modified Software: means the Software modified by at least one
+ Contribution.
+ .
+ Source Code: means all the Software's instructions and program lines to
+ which access is required so as to modify the Software.
+ .
+ Object Code: means the binary files originating from the compilation of
+ the Source Code.
+ .
+ Holder: means the holder(s) of the economic rights over the Initial
+ Software.
+ .
+ Licensee: means the Software user(s) having accepted the Agreement.
+ .
+ Contributor: means a Licensee having made at least one Contribution.
+ .
+ Licensor: means the Holder, or any other individual or legal entity, who
+ distributes the Software under the Agreement.
+ .
+ Contribution: means any or all modifications, corrections, translations,
+ adaptations and/or new functions integrated into the Software by any or
+ all Contributors, as well as any or all Internal Modules.
+ .
+ Module: means a set of sources files including their documentation that
+ enables supplementary functions or services in addition to those offered
+ by the Software.
+ .
+ External Module: means any or all Modules, not derived from the
+ Software, so that this Module and the Software run in separate address
+ spaces, with one calling the other when they are run.
+ .
+ Internal Module: means any or all Module, connected to the Software so
+ that they both execute in the same address space.
+ .
+ GNU GPL: means the GNU General Public License version 2 or any
+ subsequent version, as published by the Free Software Foundation Inc.
+ .
+ Parties: mean both the Licensee and the Licensor.
+ .
+ These expressions may be used both in singular and plural form.
+ .
+ .
+     Article 2 - PURPOSE
+ .
+ The purpose of the Agreement is the grant by the Licensor to the
+ Licensee of a non-exclusive, transferable and worldwide license for the
+ Software as set forth in Article 5 hereinafter for the whole term of the
+ protection granted by the rights over said Software. 
+ .
+ .
+     Article 3 - ACCEPTANCE
+ .
+ 3.1 The Licensee shall be deemed as having accepted the terms and
+ conditions of this Agreement upon the occurrence of the first of the
+ following events:
+ .
+     * (i) loading the Software by any or all means, notably, by
+       downloading from a remote server, or by loading from a physical
+       medium;
+     * (ii) the first time the Licensee exercises any of the rights
+       granted hereunder.
+ .
+ 3.2 One copy of the Agreement, containing a notice relating to the
+ characteristics of the Software, to the limited warranty, and to the
+ fact that its use is restricted to experienced users has been provided
+ to the Licensee prior to its acceptance as set forth in Article 3.1
+ hereinabove, and the Licensee hereby acknowledges that it has read and
+ understood it.
+ .
+ .
+     Article 4 - EFFECTIVE DATE AND TERM
+ .
+ .
+       4.1 EFFECTIVE DATE
+ .
+ The Agreement shall become effective on the date when it is accepted by
+ the Licensee as set forth in Article 3.1.
+ .
+ .
+       4.2 TERM
+ .
+ The Agreement shall remain in force for the entire legal term of
+ protection of the economic rights over the Software.
+ .
+ .
+     Article 5 - SCOPE OF RIGHTS GRANTED
+ .
+ The Licensor hereby grants to the Licensee, who accepts, the following
+ rights over the Software for any or all use, and for the term of the
+ Agreement, on the basis of the terms and conditions set forth hereinafter.
+ .
+ Besides, if the Licensor owns or comes to own one or more patents
+ protecting all or part of the functions of the Software or of its
+ components, the Licensor undertakes not to enforce the rights granted by
+ these patents against successive Licensees using, exploiting or
+ modifying the Software. If these patents are transferred, the Licensor
+ undertakes to have the transferees subscribe to the obligations set
+ forth in this paragraph.
+ .
+ .
+       5.1 RIGHT OF USE
+ .
+ The Licensee is authorized to use the Software, without any limitation
+ as to its fields of application, with it being hereinafter specified
+ that this comprises:
+ .
+    1. permanent or temporary reproduction of all or part of the Software
+       by any or all means and in any or all form.
+ .
+    2. loading, displaying, running, or storing the Software on any or
+       all medium.
+ .
+    3. entitlement to observe, study or test its operation so as to
+       determine the ideas and principles behind any or all constituent
+       elements of said Software. This shall apply when the Licensee
+       carries out any or all loading, displaying, running, transmission
+       or storage operation as regards the Software, that it is entitled
+       to carry out hereunder.
+ .
+ .
+       5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+ .
+ The right to make Contributions includes the right to translate, adapt,
+ arrange, or make any or all modifications to the Software, and the right
+ to reproduce the resulting software.
+ .
+ The Licensee is authorized to make any or all Contributions to the
+ Software provided that it includes an explicit notice that it is the
+ author of said Contribution and indicates the date of the creation thereof.
+ .
+ .
+       5.3 RIGHT OF DISTRIBUTION
+ .
+ In particular, the right of distribution includes the right to publish,
+ transmit and communicate the Software to the general public on any or
+ all medium, and by any or all means, and the right to market, either in
+ consideration of a fee, or free of charge, one or more copies of the
+ Software by any means.
+ .
+ The Licensee is further authorized to distribute copies of the modified
+ or unmodified Software to third parties according to the terms and
+ conditions set forth hereinafter.
+ .
+ .
+         5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+ .
+ The Licensee is authorized to distribute true copies of the Software in
+ Source Code or Object Code form, provided that said distribution
+ complies with all the provisions of the Agreement and is accompanied by:
+ .
+    1. a copy of the Agreement,
+ .
+    2. a notice relating to the limitation of both the Licensor's
+       warranty and liability as set forth in Articles 8 and 9,
+ .
+ and that, in the event that only the Object Code of the Software is
+ redistributed, the Licensee allows future Licensees unhindered access to
+ the full Source Code of the Software by indicating how to access it, it
+ being understood that the additional cost of acquiring the Source Code
+ shall not exceed the cost of transferring the data.
+ .
+ .
+         5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+ .
+ When the Licensee makes a Contribution to the Software, the terms and
+ conditions for the distribution of the resulting Modified Software
+ become subject to all the provisions of this Agreement.
+ .
+ The Licensee is authorized to distribute the Modified Software, in
+ source code or object code form, provided that said distribution
+ complies with all the provisions of the Agreement and is accompanied by:
+ .
+    1. a copy of the Agreement,
+ .
+    2. a notice relating to the limitation of both the Licensor's
+       warranty and liability as set forth in Articles 8 and 9,
+ .
+ and that, in the event that only the object code of the Modified
+ Software is redistributed, the Licensee allows future Licensees
+ unhindered access to the full source code of the Modified Software by
+ indicating how to access it, it being understood that the additional
+ cost of acquiring the source code shall not exceed the cost of
+ transferring the data.
+ .
+ .
+         5.3.3 DISTRIBUTION OF EXTERNAL MODULES
+ .
+ When the Licensee has developed an External Module, the terms and
+ conditions of this Agreement do not apply to said External Module, that
+ may be distributed under a separate license agreement.
+ .
+ .
+         5.3.4 COMPATIBILITY WITH THE GNU GPL
+ .
+ The Licensee can include a code that is subject to the provisions of one
+ of the versions of the GNU GPL in the Modified or unmodified Software,
+ and distribute that entire code under the terms of the same version of
+ the GNU GPL.
+ .
+ The Licensee can include the Modified or unmodified Software in a code
+ that is subject to the provisions of one of the versions of the GNU GPL,
+ and distribute that entire code under the terms of the same version of
+ the GNU GPL.
+ .
+ .
+     Article 6 - INTELLECTUAL PROPERTY
+ .
+ .
+       6.1 OVER THE INITIAL SOFTWARE
+ .
+ The Holder owns the economic rights over the Initial Software. Any or
+ all use of the Initial Software is subject to compliance with the terms
+ and conditions under which the Holder has elected to distribute its work
+ and no one shall be entitled to modify the terms and conditions for the
+ distribution of said Initial Software.
+ .
+ The Holder undertakes that the Initial Software will remain ruled at
+ least by this Agreement, for the duration set forth in Article 4.2.
+ .
+ .
+       6.2 OVER THE CONTRIBUTIONS
+ .
+ The Licensee who develops a Contribution is the owner of the
+ intellectual property rights over this Contribution as defined by
+ applicable law.
+ .
+ .
+       6.3 OVER THE EXTERNAL MODULES
+ .
+ The Licensee who develops an External Module is the owner of the
+ intellectual property rights over this External Module as defined by
+ applicable law and is free to choose the type of agreement that shall
+ govern its distribution.
+ .
+ .
+       6.4 JOINT PROVISIONS
+ .
+ The Licensee expressly undertakes:
+ .
+    1. not to remove, or modify, in any manner, the intellectual property
+       notices attached to the Software;
+ .
+    2. to reproduce said notices, in an identical manner, in the copies
+       of the Software modified or not.
+ .
+ The Licensee undertakes not to directly or indirectly infringe the
+ intellectual property rights of the Holder and/or Contributors on the
+ Software and to take, where applicable, vis-à-vis its staff, any and all
+ measures required to ensure respect of said intellectual property rights
+ of the Holder and/or Contributors.
+ .
+ .
+     Article 7 - RELATED SERVICES
+ .
+ 7.1 Under no circumstances shall the Agreement oblige the Licensor to
+ provide technical assistance or maintenance services for the Software.
+ .
+ However, the Licensor is entitled to offer this type of services. The
+ terms and conditions of such technical assistance, and/or such
+ maintenance, shall be set forth in a separate instrument. Only the
+ Licensor offering said maintenance and/or technical assistance services
+ shall incur liability therefor.
+ .
+ 7.2 Similarly, any Licensor is entitled to offer to its licensees, under
+ its sole responsibility, a warranty, that shall only be binding upon
+ itself, for the redistribution of the Software and/or the Modified
+ Software, under terms and conditions that it is free to decide. Said
+ warranty, and the financial terms and conditions of its application,
+ shall be subject of a separate instrument executed between the Licensor
+ and the Licensee.
+ .
+ .
+     Article 8 - LIABILITY
+ .
+ 8.1 Subject to the provisions of Article 8.2, the Licensee shall be
+ entitled to claim compensation for any direct loss it may have suffered
+ from the Software as a result of a fault on the part of the relevant
+ Licensor, subject to providing evidence thereof.
+ .
+ 8.2 The Licensor's liability is limited to the commitments made under
+ this Agreement and shall not be incurred as a result of in particular:
+ (i) loss due the Licensee's total or partial failure to fulfill its
+ obligations, (ii) direct or consequential loss that is suffered by the
+ Licensee due to the use or performance of the Software, and (iii) more
+ generally, any consequential loss. In particular the Parties expressly
+ agree that any or all pecuniary or business loss (i.e. loss of data,
+ loss of profits, operating loss, loss of customers or orders,
+ opportunity cost, any disturbance to business activities) or any or all
+ legal proceedings instituted against the Licensee by a third party,
+ shall constitute consequential loss and shall not provide entitlement to
+ any or all compensation from the Licensor.
+ .
+ .
+     Article 9 - WARRANTY
+ .
+ 9.1 The Licensee acknowledges that the scientific and technical
+ state-of-the-art when the Software was distributed did not enable all
+ possible uses to be tested and verified, nor for the presence of
+ possible defects to be detected. In this respect, the Licensee's
+ attention has been drawn to the risks associated with loading, using,
+ modifying and/or developing and reproducing the Software which are
+ reserved for experienced users.
+ .
+ The Licensee shall be responsible for verifying, by any or all means,
+ the suitability of the product for its requirements, its good working
+ order, and for ensuring that it shall not cause damage to either persons
+ or properties.
+ .
+ 9.2 The Licensor hereby represents, in good faith, that it is entitled
+ to grant all the rights over the Software (including in particular the
+ rights set forth in Article 5).
+ .
+ 9.3 The Licensee acknowledges that the Software is supplied "as is" by
+ the Licensor without any other express or tacit warranty, other than
+ that provided for in Article 9.2 and, in particular, without any warranty 
+ as to its commercial value, its secured, safe, innovative or relevant
+ nature.
+ .
+ Specifically, the Licensor does not warrant that the Software is free
+ from any error, that it will operate without interruption, that it will
+ be compatible with the Licensee's own equipment and software
+ configuration, nor that it will meet the Licensee's requirements.
+ .
+ 9.4 The Licensor does not either expressly or tacitly warrant that the
+ Software does not infringe any third party intellectual property right
+ relating to a patent, software or any other property right. Therefore,
+ the Licensor disclaims any and all liability towards the Licensee
+ arising out of any or all proceedings for infringement that may be
+ instituted in respect of the use, modification and redistribution of the
+ Software. Nevertheless, should such proceedings be instituted against
+ the Licensee, the Licensor shall provide it with technical and legal
+ assistance for its defense. Such technical and legal assistance shall be
+ decided on a case-by-case basis between the relevant Licensor and the
+ Licensee pursuant to a memorandum of understanding. The Licensor
+ disclaims any and all liability as regards the Licensee's use of the
+ name of the Software. No warranty is given as regards the existence of
+ prior rights over the name of the Software or as regards the existence
+ of a trademark.
+ .
+ .
+     Article 10 - TERMINATION
+ .
+ 10.1 In the event of a breach by the Licensee of its obligations
+ hereunder, the Licensor may automatically terminate this Agreement
+ thirty (30) days after notice has been sent to the Licensee and has
+ remained ineffective.
+ .
+ 10.2 A Licensee whose Agreement is terminated shall no longer be
+ authorized to use, modify or distribute the Software. However, any
+ licenses that it may have granted prior to termination of the Agreement
+ shall remain valid subject to their having been granted in compliance
+ with the terms and conditions hereof.
+ .
+ .
+     Article 11 - MISCELLANEOUS
+ .
+ .
+       11.1 EXCUSABLE EVENTS
+ .
+ Neither Party shall be liable for any or all delay, or failure to
+ perform the Agreement, that may be attributable to an event of force
+ majeure, an act of God or an outside cause, such as defective
+ functioning or interruptions of the electricity or telecommunications
+ networks, network paralysis following a virus attack, intervention by
+ government authorities, natural disasters, water damage, earthquakes,
+ fire, explosions, strikes and labor unrest, war, etc.
+ .
+ 11.2 Any failure by either Party, on one or more occasions, to invoke
+ one or more of the provisions hereof, shall under no circumstances be
+ interpreted as being a waiver by the interested Party of its right to
+ invoke said provision(s) subsequently.
+ .
+ 11.3 The Agreement cancels and replaces any or all previous agreements,
+ whether written or oral, between the Parties and having the same
+ purpose, and constitutes the entirety of the agreement between said
+ Parties concerning said purpose. No supplement or modification to the
+ terms and conditions hereof shall be effective as between the Parties
+ unless it is made in writing and signed by their duly authorized
+ representatives.
+ .
+ 11.4 In the event that one or more of the provisions hereof were to
+ conflict with a current or future applicable act or legislative text,
+ said act or legislative text shall prevail, and the Parties shall make
+ the necessary amendments so as to comply with said act or legislative
+ text. All other provisions shall remain effective. Similarly, invalidity
+ of a provision of the Agreement, for any reason whatsoever, shall not
+ cause the Agreement as a whole to be invalid.
+ .
+ .
+       11.5 LANGUAGE
+ .
+ The Agreement is drafted in both French and English and both versions
+ are deemed authentic.
+ .
+ .
+     Article 12 - NEW VERSIONS OF THE AGREEMENT
+ .
+ 12.1 Any person is authorized to duplicate and distribute copies of this
+ Agreement.
+ .
+ 12.2 So as to ensure coherence, the wording of this Agreement is
+ protected and may only be modified by the authors of the License, who
+ reserve the right to periodically publish updates or new versions of the
+ Agreement, each with a separate number. These subsequent versions may
+ address new issues encountered by Free Software.
+ .
+ 12.3 Any Software distributed under a given version of the Agreement may
+ only be subsequently distributed under the same version of the Agreement
+ or a subsequent version, subject to the provisions of Article 5.3.4.
+ .
+ .
+     Article 13 - GOVERNING LAW AND JURISDICTION
+ .
+ 13.1 The Agreement is governed by French law. The Parties agree to
+ endeavor to seek an amicable solution to any disagreements or disputes
+ that may arise during the performance of the Agreement.
+ .
+ 13.2 Failing an amicable solution within two (2) months as from their
+ occurrence, and unless emergency proceedings are necessary, the
+ disagreements or disputes shall be referred to the Paris Courts having
+ jurisdiction, by the more diligent Party.
+ .
+ .
+ Version 2.0 dated 2006-09-05.
+

Added: trunk/packages/gassst/trunk/debian/dirs
===================================================================
--- trunk/packages/gassst/trunk/debian/dirs	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/dirs	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1 @@
+usr/bin

Added: trunk/packages/gassst/trunk/debian/docs
===================================================================
--- trunk/packages/gassst/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/docs	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1 @@
+README

Added: trunk/packages/gassst/trunk/debian/gassst.1
===================================================================
--- trunk/packages/gassst/trunk/debian/gassst.1	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/gassst.1	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1,77 @@
+.TH gassst 1  "January 4, 2012" "version 1.28" "USER COMMANDS"
+.SH NAME
+gassst \- Global Alignment Short Sequence Search Tool
+.SH SYNOPSIS
+.B gassst -d <bank_file> -i <query_file> -o <output_file> -p <identity_percentage> [options]
+
+.I [-w <size_seed>] [-m <output_format>] [-l <complexity_filter>] [-t <size_partition>] [-r <reverse_complement>] [-g <gaps_number>] [-n <thread_number>] [-h <max_hits_per_read>] [-s <sensitivity level>] [-b <output best alignments>] [-z <obscure option : bitstat>]
+.SH DESCRIPTION
+GASSST finds global alignments of short DNA sequences against large DNA banks.
+
+The program takes as inputs 2 banks in FASTA format:
+
+- bank_file:  a collection of DNA sequences of any length (from short EST sequence to full genome)
+
+- query file: a collection of very short DNA sequences
+
+.PP
+.SH MANDATORY OPTIONS
+.TP
+\-d <bank_file>
+(string) Name of a DNA sequence bank in FASTA format
+.TP
+\-i <query_file>
+(string) Name of a DNA sequence bank in FASTA format - Short sequences
+.TP
+\-o <output_file>
+(string) Name of the output file to store the results
+.TP
+\-p <identity_percentage>
+(integer) Minimum percentage of identity. Must be in the interval [0 100]
+.SH ADDITIONAL OPTIONS
+.TP
+\-w <size_seed>
+(integer) Size of the anchoring seed. Must be in the interval [6 20] (Default : automatic)
+.TP
+\-m <output_format>
+(integer) 1 = standard Gassst format. 0 = human readable format. 8 = blast-like m8 format (Default : 1)
+.TP
+\-n <thread number>
+(integer) Number of processor threads (Default : 1)
+.TP
+\-l <complexity_filter>
+(integer) 0 = low complexity filter off. 1 = low complexity filter on (Default : on)
+.TP
+\-t <size_partition>
+(integer) Maximum size for the bank's partitions in Megabytes. Must be in the interval [1;1 600] (Default : 2% of the RAM size, recommended)
+.TP
+\-r <reverse_complement>
+(integer) 0 = Disable the revert complement research, 1 = Enable the revert complement research (Default : 1)
+.TP
+\-g <gaps_number>
+(integer) Number of gaps allowed. (Default : maximum allowed by identity percentage)
+.TP
+\-h <max alignment per read>
+(integer) Maximum number of alignment per query. 0 means no limit (Default : 100)
+.TP
+\-s <sensitivity level>
+(integer) Sensitivity level, in [0-5]. 0 is fastest, 5 is best sensitivity (Default : 2)
+.TP
+\-b <output best alignments>
+(integer) 1 = output best alignments. 0 = output random alignments, slightly faster (Default : 1)
+.SH USAGE
+Tool usage is available in /usr/share/doc/gassst/README.
+.PP
+.SH EXAMPLE
+gassst \-d  genome.fasta  \-i reads.fasta  \-o output  \-p 90 
+.SH SAM CONVERSION
+gassst_to_sam output output.sam
+.SH CITING
+GASSST: global alignment short sequence search tool, Guillaume Rizk,Dominique Lavanier,
+Bioinformatics (2010) 26 (20): 2534-2540 doi: 10.1093/bioinformatics/btq485
+.PP
+.SH AUTHOR
+Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
+Guillaume Rizk,Dominique Lavanier - gassst
+
+

Added: trunk/packages/gassst/trunk/debian/gassst.install
===================================================================
--- trunk/packages/gassst/trunk/debian/gassst.install	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/gassst.install	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1,2 @@
+gassst usr/bin
+gassst_to_sam  usr/bin

Added: trunk/packages/gassst/trunk/debian/gassst.manpages
===================================================================
--- trunk/packages/gassst/trunk/debian/gassst.manpages	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/gassst.manpages	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1,2 @@
+debian/gassst.1
+debian/gassst_to_sam.1

Added: trunk/packages/gassst/trunk/debian/gassst_to_sam.1
===================================================================
--- trunk/packages/gassst/trunk/debian/gassst_to_sam.1	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/gassst_to_sam.1	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1,18 @@
+.TH gassst_to_sam 1  "January 4, 2012" "version 1.28" "USER COMMANDS"
+.SH NAME
+gassst_to_sam \- Convert gassst output to SAM format
+.SH SYNOPSIS
+.B gassst_to_sam <gassst_outputfile>  <output_file.sam>
+.SH WARNING
+The gassst_to_sam utility currently only takes as input the standard Gassst 
+output format ("1"), not format "0" or "8".
+.PP
+.SH CITING
+GASSST: global alignment short sequence search tool, Guillaume Rizk,Dominique Lavanier,
+Bioinformatics (2010) 26 (20): 2534-2540 doi: 10.1093/bioinformatics/btq485
+.PP
+.SH AUTHOR
+Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
+Guillaume Rizk,Dominique Lavanier - gassst
+
+

Added: trunk/packages/gassst/trunk/debian/rules
===================================================================
--- trunk/packages/gassst/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/rules	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1,17 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+	dh $@ 
+
+override_dh_install:
+	mv Gassst gassst
+	dh_install
+
+override_dh_clean:
+	dh_clean
+	rm -f gassst
+	rm -f gassst_to_sam


Property changes on: trunk/packages/gassst/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/gassst/trunk/debian/source/format
===================================================================
--- trunk/packages/gassst/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/source/format	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/gassst/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/gassst/trunk/debian/upstream-metadata.yaml	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/upstream-metadata.yaml	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1,12 @@
+Contact: Dominique Lavanier <dominique.lavanier at irisa.fr>
+DOI: 10.1093/bioinformatics/btq485
+Homepage: http://www.irisa.fr/symbiose/projects/gassst/
+Name: GASSST
+Reference:
+ author: Guillaume Rizk and Dominique Lavanier
+ title: GASSST: global alignment short sequence search tool
+ journal: Bioinformatics
+ volume: 20
+ number: 36
+ year: 2010
+ URL: http://bioinformatics.oxfordjournals.org/content/26/20/2534.abstract?keytype=ref&ijkey=f5zH80QsuCqixRH

Added: trunk/packages/gassst/trunk/debian/watch
===================================================================
--- trunk/packages/gassst/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/gassst/trunk/debian/watch	2012-01-04 15:20:59 UTC (rev 9172)
@@ -0,0 +1,7 @@
+# Compulsory line, this is a version 3 file
+version=3
+
+# Uncomment to examine a Webpage
+# <Webpage URL> <string match>
+http://www.irisa.fr/symbiose/projects/gassst/ Gassst_v(.*)\.tar\.gz
+




More information about the debian-med-commit mailing list