[med-svn] [Git][med-team/pal2nal][master] 3 commits: New upstream version 14.1

Thu May 10 00:19:41 BST 2018

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 (mikita at genome.med.kyoto-u.ac.jp)   #
+#               Mikita Suyama (mikita at bioreg.kyushu-u.ac.jp)      #
 #                                                                 #
 #=================================================================#
 
@@ -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: mikita at genome.med.kyoto-u.ac.jp
+  Medical Institute of Bioregulation
+  Kyushu University,
+  812-8582 Fukuoka, JAPAN
+  tel: +81 92 642 6384
+  fax: +81 92 642 6562
+  email: mikita at bioreg.kyushu-u.ac.jp
 


=====================================
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 <steffen_moeller at gmx.de>  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 <steffen_moeller at gmx.de>  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 <moeller at debian.org>  Thu, 10 May 2018 01:05:44 +0200
+
+pal2nal (14-1) UNRELEASED; urgency=low
+
+  * Initiated packaging.
+
  -- Steffen Moeller <moeller at debian.org>  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 <mikita at bioreg.kyushu-u.ac.jp>
-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 <mikita at bioreg.kyushu-u.ac.jp>
                      David Torrents, and Peer Bork and their respective employing institute
-License: to_be_clarified
+License: GPL-2
 
 Files: debian/*
-Copyright:  Steffen Moeller <moeller at debian.org> on Tue, 23 Nov 2010 16:18:36 +0100
-License: GPL-3+
+Copyright:  Steffen Moeller <moeller at debian.org>
+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 <mikita at bioreg.kyushu-u.ac.jp>
 #
-#    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
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