Steffen Möller pushed to branch master at Debian Med / pal2nal
Commits: 4f7f0eac by Steffen Moeller at 2018-05-10T00:58:29+02:00 New upstream version 14.1 - - - - - fc89a99b by Steffen Moeller at 2018-05-10T00:58:30+02:00 Update upstream source from tag 'upstream/14.1' Update to upstream version '14.1' with Debian dir 09be4b1f79b78f934e60f7375b82d8ab283ac112 - - - - - 81d3a292 by Steffen Moeller at 2018-05-10T01:18:41+02:00 Upload of 14.1 - - - - - 6 changed files: - README - debian/README.Debian - debian/changelog - debian/copyright - debian/pal2nal.1 - pal2nal.pl Changes: ===================================== README ===================================== --- a/README +++ b/README @@ -14,8 +14,9 @@ # version 12.2 September 9, 2009 # # version 13.0 July 26, 2010 # # version 14.0 December 2, 2011 # +# version 14.1 October 17, 2017 # # # -# Mikita Suyama ([email protected]) # +# Mikita Suyama ([email protected]) # # # #=================================================================# @@ -35,6 +36,9 @@ The resulting codon-based DNA alignment can further be subjected to the calculation of synonymous (Ks) and non-synonymous (Ka) substitution rates. +The script is licensed under GPL v2. + + #-----------# # Reference @@ -176,7 +180,7 @@ Example: http://www.bork.embl.de/pal2nal or -http://www.genome.med.kyoto-u.ac.jp/cgi-bin/suyama/pal2nal/index.cgi +http://www.genome.med.kyoto-u.ac.jp/cgi-bin/suyama/pal2nal/index.cgi (not working) #---------# @@ -186,10 +190,10 @@ http://www.genome.med.kyoto-u.ac.jp/cgi-bin/suyama/pal2nal/index.cgi If you have any questions or comments, please email me: Mikita Suyama - Center for Genomic Medicine, - Graduate School of Medicine, Kyoto University, - 606-8501 Kyoto, JAPAN - tel: +81 75 753 4383 - fax: +81 75 753 4382 - email: [email protected] + Medical Institute of Bioregulation + Kyushu University, + 812-8582 Fukuoka, JAPAN + tel: +81 92 642 6384 + fax: +81 92 642 6562 + email: [email protected] ===================================== debian/README.Debian ===================================== --- a/debian/README.Debian +++ b/debian/README.Debian @@ -9,3 +9,8 @@ lose its .pl suffix. The answer is most likely "yes", but would require some synchronisation e.g. with the bioperl developers. -- Steffen Moeller <[email protected]> Tue, 23 Nov 2010 16:18:36 +0100 + +Updated opinion: The .pl suffix better remains available. There are too +many scrips expecting it. + + -- Steffen Moeller <[email protected]> Thu, 10 May 2018 01:09:29 +0200 ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,5 +1,13 @@ -pal2nal (14-1) UNRELEASED; urgency=low +pal2nal (14.1-1) unstable; urgency=low * Initial release (Closes: #604701) + * New upstream version clarified license. + + -- Steffen Moeller <[email protected]> Thu, 10 May 2018 01:05:44 +0200 + +pal2nal (14-1) UNRELEASED; urgency=low + + * Initiated packaging. + -- Steffen Moeller <[email protected]> Tue, 23 Nov 2010 16:18:36 +0100 ===================================== debian/copyright ===================================== --- a/debian/copyright +++ b/debian/copyright @@ -1,12 +1,29 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Contact: Mikita Suyama <[email protected]> -Source: http://www.bork.embl.de/pal2nal/distribution/ +Source: http://www.bork.embl.de/pal2nal/distribution/ to which upstream has no access, found it on + https://sourceforge.net/projects/sboppetrov/files/pal2nal/pal2nal.v14.1.tar.gz/download Files: * Copyright: 2004-2011 Mikita Suyama <[email protected]> David Torrents, and Peer Bork and their respective employing institute -License: to_be_clarified +License: GPL-2 Files: debian/* -Copyright: Steffen Moeller <[email protected]> on Tue, 23 Nov 2010 16:18:36 +0100 -License: GPL-3+ +Copyright: Steffen Moeller <[email protected]> +License: GPL-2 + +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 <https://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". ===================================== debian/pal2nal.1 ===================================== --- a/debian/pal2nal.1 +++ b/debian/pal2nal.1 @@ -1,7 +1,7 @@ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. .TH PAL2NAL.PL "1" "November 2010" "pal2nal.pl " "User Commands" .SH NAME -pal2nal.pl \- manual page for pal2nal.pl +pal2nal.pl \- use insight from protein alignment for nucleotide alignment .SH SYNOPSIS .B pal2nal.pl \fIpep.aln nuc.fasta \fR[\fInuc.fasta\fR...] [\fIoptions\fR] ===================================== pal2nal.pl ===================================== --- a/pal2nal.pl +++ b/pal2nal.pl @@ -1,6 +1,13 @@ #!/usr/bin/perl +# pal2nal.pl (c) 2017 Mikita Suyama <[email protected]> # -# pal2nal.pl (v14) Mikita Suyama +# #----------------------------------------# +# This script is licensed under GPL v2.0 +# #----------------------------------------# +# +# +# +# pal2nal.pl (v14.1) Mikita Suyama # # Usage: pal2nal.pl pep.aln nuc.fasta [nuc.fasta...] [options] > output # @@ -56,6 +63,10 @@ # NUC1 GCTTGTGATGAATTTGGTGCTCGTCATG--GGG---TTTTAA # NUC2 GCGGG-GACGACTGG---GCGTAGCAC---GGGGG-TTTTGA # +# +# v14.1 +# - licensed under GPL v2.0 +# 2017/10/17 # v14. # - NCBI GenBank codon table # 1 Universal code View it on GitLab: https://salsa.debian.org/med-team/pal2nal/compare/42ac642d15f464b73e9587aa4d1fd06d45181cfa...81d3a2927a73c556e72e7f917c7b24dadd4b35a7 --- View it on GitLab: https://salsa.debian.org/med-team/pal2nal/compare/42ac642d15f464b73e9587aa4d1fd06d45181cfa...81d3a2927a73c556e72e7f917c7b24dadd4b35a7 You're receiving this email because of your account on salsa.debian.org.
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