Author: plessy Date: 2012-01-07 04:53:35 +0000 (Sat, 07 Jan 2012) New Revision: 9189
Added: trunk/packages/mira/tags/3.4.0.1-2/ trunk/packages/mira/tags/3.4.0.1-2/debian/changelog trunk/packages/mira/tags/3.4.0.1-2/debian/control trunk/packages/mira/tags/3.4.0.1-2/debian/copyright Removed: trunk/packages/mira/tags/3.4.0.1-2/debian/changelog trunk/packages/mira/tags/3.4.0.1-2/debian/control trunk/packages/mira/tags/3.4.0.1-2/debian/copyright Log: [svn-buildpackage] Tagging mira 3.4.0.1-2 Deleted: trunk/packages/mira/tags/3.4.0.1-2/debian/changelog =================================================================== --- trunk/packages/mira/trunk/debian/changelog 2012-01-06 22:28:28 UTC (rev 9184) +++ trunk/packages/mira/tags/3.4.0.1-2/debian/changelog 2012-01-07 04:53:35 UTC (rev 9189) @@ -1,84 +0,0 @@ -mira (3.4.0.1-2) UNRELEASED; urgency=low - - * Remove two patches: - - read_default_constructor.patch which introduces a duplicate - bposhashstat_t() definition - - fix_duplicate_bposhashstat_t_definition.patch which removes - this duplicate afterwards - - -- Andreas Tille <[email protected]> Fri, 09 Dec 2011 09:05:53 +0100 - -mira (3.4.0.1-1) unstable; urgency=low - - * New upstream version - Closes: #648762 (at least if I'm not missleaded - feel free to reopen) - * debian/control: - - Added myself to Uploaders - - Depends: libtcmalloc-minimal0 [i386 amd64] - Thanks for the patch to Michael Terry <[email protected]> - however I left out powerpc where libtcmalloc-minimal0 is not - available - Closes: #649093 - - Fixed Vcs fields - * debian/patches/fix_duplicate_bposhashstat_t_definition.patch - Remove duplicate defintion of bposhashstat_t() - - -- Andreas Tille <[email protected]> Thu, 08 Dec 2011 08:50:19 +0100 - -mira (3.4.0-3ubuntu1) lucid; urgency=low - - * Small fix to dependencies - there is no "mira" binary package - - -- Tim Booth <[email protected]> Fri, 02 Dec 2011 15:00:35 +0000 - -mira (3.4.0-3) unstable; urgency=low - - * Rendering Tim's additions available for Debian - - -- Steffen Moeller <[email protected]> Sat, 03 Sep 2011 01:02:10 +0200 - -mira (3.4.0-2ubuntu5) lucid; urgency=low - - * Small fix to clean target and suppress warnings - on Lucid backport. - * Fixed missing dependency which caused misleading configure - failure. - * Yet another missing build dep - flex and xxd - - -- Tim Booth <[email protected]> Tue, 30 Aug 2011 17:17:11 +0100 - -mira (3.4.0-2) unstable; urgency=low - - * Fixing source tree (removed PDF with no source) - - -- Steffen Moeller <[email protected]> Mon, 29 Aug 2011 22:54:53 +0200 - -mira (3.4.0-1) UNRELEASED; urgency=low - - * New upstream version. - - added default constructor to avoid FTBFS - * Sposoring Tim's work for Debian - * Using 3.0 (quilt) source format for bz2 upstream - - -- Steffen Moeller <[email protected]> Tue, 23 Aug 2011 20:46:32 +0200 - -mira (3.4rc3-2) lucid; urgency=low - - * Version 3.2.1.8 has been removed from SF.net. Packaging the - latest RC instead. - * Fixed linking against tcmalloc (see README) - * Fixed build of docs - HTML is installed in mira-doc - - -- Tim Booth <[email protected]> Fri, 19 Aug 2011 12:35:12 +0100 - -mira (3.2.1.8-1) UNRELEASED; urgency=low - - * Initial release (Closes: #435915) - - -- Steffen Moeller <[email protected]> Fri, 04 Mar 2011 11:55:25 +0100 - -mira (3~rc2-1) UNRELEASED; urgency=low - - * Initial packaging. - - -- Charles Plessy <[email protected]> Tue, 08 Sep 2009 13:35:31 +0900 Copied: trunk/packages/mira/tags/3.4.0.1-2/debian/changelog (from rev 9188, trunk/packages/mira/trunk/debian/changelog) =================================================================== --- trunk/packages/mira/tags/3.4.0.1-2/debian/changelog (rev 0) +++ trunk/packages/mira/tags/3.4.0.1-2/debian/changelog 2012-01-07 04:53:35 UTC (rev 9189) @@ -0,0 +1,90 @@ +mira (3.4.0.1-2) unstable; urgency=low + + [ Andreas Tille ] + * Remove two patches: + - read_default_constructor.patch which introduces a duplicate + bposhashstat_t() definition + - fix_duplicate_bposhashstat_t_definition.patch which removes + this duplicate afterwards + + [ Charles Plessy ] + * Removed unconditional dependency on libtcmalloc-minimal0 (debian/control). + Closes: #654884 + * Machine-readable debian/copyright file. + + -- Charles Plessy <[email protected]> Sat, 07 Jan 2012 13:24:48 +0900 + +mira (3.4.0.1-1) unstable; urgency=low + + * New upstream version + Closes: #648762 (at least if I'm not mislead - feel free to reopen) + * debian/control: + - Added myself to Uploaders + - Depends: libtcmalloc-minimal0 [i386 amd64] + Thanks for the patch to Michael Terry <[email protected]> + however I left out powerpc where libtcmalloc-minimal0 is not + available + Closes: #649093 + - Fixed Vcs fields + * debian/patches/fix_duplicate_bposhashstat_t_definition.patch + Remove duplicate definition of bposhashstat_t() + + -- Andreas Tille <[email protected]> Thu, 08 Dec 2011 08:50:19 +0100 + +mira (3.4.0-3ubuntu1) lucid; urgency=low + + * Small fix to dependencies - there is no "mira" binary package + + -- Tim Booth <[email protected]> Fri, 02 Dec 2011 15:00:35 +0000 + +mira (3.4.0-3) unstable; urgency=low + + * Rendering Tim's additions available for Debian + + -- Steffen Moeller <[email protected]> Sat, 03 Sep 2011 01:02:10 +0200 + +mira (3.4.0-2ubuntu5) lucid; urgency=low + + * Small fix to clean target and suppress warnings + on Lucid backport. + * Fixed missing dependency which caused misleading configure + failure. + * Yet another missing build dep - flex and xxd + + -- Tim Booth <[email protected]> Tue, 30 Aug 2011 17:17:11 +0100 + +mira (3.4.0-2) unstable; urgency=low + + * Fixing source tree (removed PDF with no source) + + -- Steffen Moeller <[email protected]> Mon, 29 Aug 2011 22:54:53 +0200 + +mira (3.4.0-1) UNRELEASED; urgency=low + + * New upstream version. + - added default constructor to avoid FTBFS + * Sponsoring Tim's work for Debian + * Using 3.0 (quilt) source format for bz2 upstream + + -- Steffen Moeller <[email protected]> Tue, 23 Aug 2011 20:46:32 +0200 + +mira (3.4rc3-2) lucid; urgency=low + + * Version 3.2.1.8 has been removed from SF.net. Packaging the + latest RC instead. + * Fixed linking against tcmalloc (see README) + * Fixed build of docs - HTML is installed in mira-doc + + -- Tim Booth <[email protected]> Fri, 19 Aug 2011 12:35:12 +0100 + +mira (3.2.1.8-1) UNRELEASED; urgency=low + + * Initial release (Closes: #435915) + + -- Steffen Moeller <[email protected]> Fri, 04 Mar 2011 11:55:25 +0100 + +mira (3~rc2-1) UNRELEASED; urgency=low + + * Initial packaging. + + -- Charles Plessy <[email protected]> Tue, 08 Sep 2009 13:35:31 +0900 Deleted: trunk/packages/mira/tags/3.4.0.1-2/debian/control =================================================================== --- trunk/packages/mira/trunk/debian/control 2012-01-06 22:28:28 UTC (rev 9184) +++ trunk/packages/mira/tags/3.4.0.1-2/debian/control 2012-01-07 04:53:35 UTC (rev 9189) @@ -1,72 +0,0 @@ -Source: mira -Section: science -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -DM-Upload-Allowed: yes -Uploaders: Charles Plessy <[email protected]>, Steffen Moeller <[email protected]>, - Tim Booth <[email protected]>, Andreas Tille <[email protected]> -Build-Depends: debhelper (>= 7.0.50~), autotools-dev, dblatex, docbook-xsl, - libboost-thread-dev, libboost-regex-dev, libexpat1-dev, - libtcmalloc-minimal0 [i386 amd64], perl, quilt (>= 0.46-7~), flex, - vim-common, zlib1g-dev -Standards-Version: 3.9.2 -Homepage: http://chevreux.org/projects_mira.html -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mira/trunk/ -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mira/trunk/ - -Package: mira-assembler -Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends}, libtcmalloc-minimal0 -Suggests: mira-examples, mira-doc -Description: Whole Genome Shotgun and EST Sequence Assembler - The mira genome fragment assembler is a specialised assembler for - sequencing projects classified as 'hard' due to high number of similar - repeats. For expressed sequence tags (ESTs) transcripts, miraEST is - specialised on reconstructing pristine mRNA transcripts while - detecting and classifying single nucleotide polymorphisms (SNP) - occuring in different variations thereof. - . - The assembler is routinely used for such various tasks as mutation - detection in different cell types, similarity analysis of transcripts - between organisms, and pristine assembly of sequences from various - sources for oligo design in clinical microarray experiments. - . - The package provides the following executables: - Binaries provided: - * mira: for assembly of genome sequences - * miramem: estimating memory needed to assemble projects. Realised through - link to mira. - * convert_project: for converting project file types into other types - * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some - frequently used file converters (realised through links to convert_project) - * scftool: set of tools useful when working with SCF trace files - * fastatool: set of tools useful when working with FASTA trace files - . - Scripts provided: - * fasta2frag.tcl: fragmenting sequences into smaller, overlapping - subsequences. Useful for simulating shotgun sequences. Can create - subsequences in both directions (/default) and also paired-end sequences. - * fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and - a file with names of reads, select the sequences from the input FASTA (and - quality file) and writes them to an output FASTA - * fastqselect.tcl: like fastaselect.tcl, only for FASTQ - * fixACE4consed.tcl: Consed has a bug which incapacitates it from reading - consensus tags in ACE files written by the MIRA assembler (and possibly - other programs). This script massages an ACE file so that consed can read - the consensus tags. - - -Package: mira-examples -Architecture: all -Depends: ${misc:Depends} -Suggests: mira-assembler, mira-doc -Description: files to experiment with the mira assembler - A series of files to exploit the functionality of mira. - -Package: mira-doc -Section: doc -Architecture: all -Depends: ${misc:Depends} -Suggests: mira-assembler -Description: documentation for the mira assembler - An HTML book introducing to mira. Copied: trunk/packages/mira/tags/3.4.0.1-2/debian/control (from rev 9185, trunk/packages/mira/trunk/debian/control) =================================================================== --- trunk/packages/mira/tags/3.4.0.1-2/debian/control (rev 0) +++ trunk/packages/mira/tags/3.4.0.1-2/debian/control 2012-01-07 04:53:35 UTC (rev 9189) @@ -0,0 +1,72 @@ +Source: mira +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Charles Plessy <[email protected]>, Steffen Moeller <[email protected]>, + Tim Booth <[email protected]>, Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 7.0.50~), autotools-dev, dblatex, docbook-xsl, + libboost-thread-dev, libboost-regex-dev, libexpat1-dev, + libtcmalloc-minimal0 [i386 amd64], perl, quilt (>= 0.46-7~), flex, + vim-common, zlib1g-dev +Standards-Version: 3.9.2 +Homepage: http://chevreux.org/projects_mira.html +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mira/trunk/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mira/trunk/ + +Package: mira-assembler +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: mira-examples, mira-doc +Description: Whole Genome Shotgun and EST Sequence Assembler + The mira genome fragment assembler is a specialised assembler for + sequencing projects classified as 'hard' due to high number of similar + repeats. For expressed sequence tags (ESTs) transcripts, miraEST is + specialised on reconstructing pristine mRNA transcripts while + detecting and classifying single nucleotide polymorphisms (SNP) + occuring in different variations thereof. + . + The assembler is routinely used for such various tasks as mutation + detection in different cell types, similarity analysis of transcripts + between organisms, and pristine assembly of sequences from various + sources for oligo design in clinical microarray experiments. + . + The package provides the following executables: + Binaries provided: + * mira: for assembly of genome sequences + * miramem: estimating memory needed to assemble projects. Realised through + link to mira. + * convert_project: for converting project file types into other types + * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some + frequently used file converters (realised through links to convert_project) + * scftool: set of tools useful when working with SCF trace files + * fastatool: set of tools useful when working with FASTA trace files + . + Scripts provided: + * fasta2frag.tcl: fragmenting sequences into smaller, overlapping + subsequences. Useful for simulating shotgun sequences. Can create + subsequences in both directions (/default) and also paired-end sequences. + * fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and + a file with names of reads, select the sequences from the input FASTA (and + quality file) and writes them to an output FASTA + * fastqselect.tcl: like fastaselect.tcl, only for FASTQ + * fixACE4consed.tcl: Consed has a bug which incapacitates it from reading + consensus tags in ACE files written by the MIRA assembler (and possibly + other programs). This script massages an ACE file so that consed can read + the consensus tags. + + +Package: mira-examples +Architecture: all +Depends: ${misc:Depends} +Suggests: mira-assembler, mira-doc +Description: files to experiment with the mira assembler + A series of files to exploit the functionality of mira. + +Package: mira-doc +Section: doc +Architecture: all +Depends: ${misc:Depends} +Suggests: mira-assembler +Description: documentation for the mira assembler + An HTML book introducing to mira. Deleted: trunk/packages/mira/tags/3.4.0.1-2/debian/copyright =================================================================== --- trunk/packages/mira/trunk/debian/copyright 2012-01-06 22:28:28 UTC (rev 9184) +++ trunk/packages/mira/tags/3.4.0.1-2/debian/copyright 2012-01-07 04:53:35 UTC (rev 9189) @@ -1,63 +0,0 @@ -Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’. - -Source: http://jaist.dl.sourceforge.net/project/mira-assembler/MIRA/V3rc2/mira-3rc2.tar.bz2 - - -© 1997-2000 for MIRA V1.x and EdIt: Bastien Chevreux, Thomas Pfisterer, -Deutsches Krebsforschungszentrum Heidelberg -- Dept. of Molecular -Biophysics. -© 2001-2007 for MIRA V2.x: Bastien Chevreux. - -Author of MIRA - -Bastien Chevreux, formerly at the German Cancer Research Center (Deutsches - Krebsforschungsinstitut, DKFZ) in Heidelberg, DE - Now at DSM Nutritional Products AG, Kaiseraugst, CH - - -Author of EdIt - -Thomas Pfisterer, formerly at the German Cancer Research Center (Deutsches - Krebsforschungsinstitut, DKFZ) in Heidelberg. DE - Now at MWG Biotech AG, Ebersberg, DE - - -MIRA, EdIt and accompanying programs of the package are licenced under the GPL -version 2, both in source code and binaries. - -License: - - 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 package; if not, write to the Free Software - Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA - -On Debian systems, the complete text of the GNU General -Public License can be found in `/usr/share/common-licenses/GPL'. - -The file src/io/scf.H uses part of a file from the `Staden package', which is -released under the following terms: - - * Copyright (c) Medical Research Council 1994. All rights reserved. - * - * Permission to use, copy, modify and distribute this software and its - * documentation for any purpose is hereby granted without fee, provided that - * this copyright and notice appears in all copies. - * - * This file was written by James Bonfield, Simon Dear, Rodger Staden, - * as part of the Staden Package at the MRC Laboratory of Molecular - * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom. - * - * MRC disclaims all warranties with regard to this software. - -The Debian packaging is © 2007, Charles Plessy <[email protected]> and -is licensed under as if it were public domain. Copied: trunk/packages/mira/tags/3.4.0.1-2/debian/copyright (from rev 9187, trunk/packages/mira/trunk/debian/copyright) =================================================================== --- trunk/packages/mira/tags/3.4.0.1-2/debian/copyright (rev 0) +++ trunk/packages/mira/tags/3.4.0.1-2/debian/copyright 2012-01-07 04:53:35 UTC (rev 9189) @@ -0,0 +1,52 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Source: http://jaist.dl.sourceforge.net/project/mira-assembler/MIRA/V3rc2/mira-3rc2.tar.bz2 + +Files: * +Copyright: © 1997-2000 for MIRA V1.x and EdIt: Bastien Chevreux, Thomas Pfisterer, Deutsches Krebsforschungszentrum Heidelberg -- Dept. of Molecula Biophysics. + © 2001-2007 for MIRA V2.x: Bastien Chevreux. +License: GPL-2+ +Comment: + Author of MIRA + . + Bastien Chevreux, formerly at the German Cancer Research Center (Deutsches + Krebsforschungsinstitut, DKFZ) in Heidelberg, DE + Now at DSM Nutritional Products AG, Kaiseraugst, CH + . + . + Author of EdIt + . + Thomas Pfisterer, formerly at the German Cancer Research Center (Deutsches + Krebsforschungsinstitut, DKFZ) in Heidelberg. DE + Now at MWG Biotech AG, Ebersberg, DE + +Files: src/io/scf.H +Copyright: © Medical Research Council 1994 +License: staden + Permission to use, copy, modify and distribute this software and its + documentation for any purpose is hereby granted without fee, provided that + this copyright and notice appears in all copies. + . + This file was written by James Bonfield, Simon Dear, Rodger Staden, + as part of the Staden Package at the MRC Laboratory of Molecular + Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom. + . + MRC disclaims all warranties with regard to this software. +Comment: uses part of a file from the `Staden package'. + +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 package; if not, write to the Free Software + Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA +Comment: On Debian systems, the complete text of the GNU General Public + License version 2 can be found in `/usr/share/common-licenses/GPL-2'. + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
