[med-svn] [pal2nal] 14/14: Re-inject debian/ dir
Andreas Tille
tille at debian.org
Sun Jan 15 10:12:19 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository pal2nal.
commit a9d37484c0da19e96957678488cb8ff817d00b12
Author: Andreas Tille <tille at debian.org>
Date: Sun Jan 15 11:11:37 2017 +0100
Re-inject debian/ dir
---
debian/README.Debian | 11 +++++
debian/changelog | 5 +++
debian/compat | 1 +
debian/control | 28 +++++++++++++
debian/copyright | 12 ++++++
debian/docs | 1 +
debian/examples | 2 +
debian/manpages | 1 +
debian/pal2nal.1 | 107 +++++++++++++++++++++++++++++++++++++++++++++++
debian/pal2nal.install | 1 +
debian/rules | 13 ++++++
debian/source/format | 1 +
debian/upstream/metadata | 11 +++++
debian/watch | 4 ++
14 files changed, 198 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..0146bc0
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,11 @@
+pal2nal for Debian
+------------------
+
+This package comes without a license and as such remains unredistributable
+untils this has been clarified with upstream.
+
+It remains unclear if the "binary" should be renamed to pal2nal, ie.
+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
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..1167b83
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+pal2nal (14-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #604701)
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 23 Nov 2010 16:18:36 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..4fd02a3
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,28 @@
+Source: pal2nal
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Pjotr Prins <pjotr.debian at thebird.nl>,
+ Steffen Moeller <moeller at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 10)
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pal2nal.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/pal2nal.git
+Homepage: http://www.bork.embl.de/pal2nal
+
+Package: pal2nal
+Architecture: all
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Recommends: paml
+Description: converts proteins to genomic DNA alignment
+ PAL2NAL is a program that converts a multiple sequence alignment
+ of proteins and the corresponding DNA (or mRNA) sequences into
+ a codon-based DNA alignment. The program automatically assigns
+ the corresponding codon sequence even if the input DNA sequence
+ has mismatches with the input protein sequence, or contains UTRs,
+ polyA tails. It can also deal with frame shifts in the input
+ alignment, which is suitable for the analysis of pseudogenes.
+ The resulting codon-based DNA alignment can further be subjected
+ to the calculation of synonymous (Ks) and non-synonymous (Ka)
+ substitution rates.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..8402949
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,12 @@
+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/
+
+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
+
+Files: debian/*
+Copyright: Steffen Moeller <moeller at debian.org> on Tue, 23 Nov 2010 16:18:36 +0100
+License: GPL-3+
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..e845566
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..c4a1e5b
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1,2 @@
+test.aln
+test.nuc
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..7072627
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/pal2nal.1
diff --git a/debian/pal2nal.1 b/debian/pal2nal.1
new file mode 100644
index 0000000..80ebb3b
--- /dev/null
+++ b/debian/pal2nal.1
@@ -0,0 +1,107 @@
+.\" 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
+.SH SYNOPSIS
+.B pal2nal.pl
+\fIpep.aln nuc.fasta \fR[\fInuc.fasta\fR...] [\fIoptions\fR]
+.SH DESCRIPTION
+pal2nal.pl (v13)
+.TP
+pep.aln:
+protein alignment either in CLUSTAL or FASTA format
+.TP
+nuc.fasta:
+DNA sequences (single multi\-fasta or separated files)
+.TP
+Options:
+\fB\-h\fR Show help
+.IP
+\fB\-output\fR (clustal|paml|fasta|codon)
+.IP
+Output format; default = clustal
+.TP
+\fB\-blockonly\fR
+Show only user specified blocks
+\&'#' under CLUSTAL alignment (see example)
+.TP
+\fB\-nogap\fR
+remove columns with gaps and inframe stop codons
+.TP
+\fB\-nomismatch\fR
+remove mismatched codons (mismatch between
+pep and cDNA) from the output
+.IP
+\fB\-codontable\fR (universal|vmitochondria)
+.IP
+Codon table
+.IP
+\- universal (default)
+\- vmitochondria \-> vertebrate mitochondrial
+.TP
+\fB\-html\fR
+HTML output (only for the web server)
+.TP
+\fB\-nostderr\fR
+No STDERR messages (only for the web server)
+.IP
+\- sequence order in pep.aln and nuc.fasta should be the same.
+.IP
+\- IDs in pep.aln are used in the output.
+.PP
+pal2nal.pl (v13)
+.PP
+Usage: pal2nal.pl pep.aln nuc.fasta [nuc.fasta...] [options]
+.TP
+pep.aln:
+protein alignment either in CLUSTAL or FASTA format
+.TP
+nuc.fasta:
+DNA sequences (single multi\-fasta or separated files)
+.TP
+Options:
+\fB\-h\fR Show help
+.IP
+\fB\-output\fR (clustal|paml|fasta|codon)
+.IP
+Output format; default = clustal
+.TP
+\fB\-blockonly\fR
+Show only user specified blocks
+\&'#' under CLUSTAL alignment (see example)
+.TP
+\fB\-nogap\fR
+remove columns with gaps and inframe stop codons
+.TP
+\fB\-nomismatch\fR
+remove mismatched codons (mismatch between
+pep and cDNA) from the output
+.IP
+\fB\-codontable\fR (universal|vmitochondria)
+.IP
+Codon table
+.IP
+\- universal (default)
+\- vmitochondria \-> vertebrate mitochondrial
+.TP
+\fB\-html\fR
+HTML output (only for the web server)
+.TP
+\fB\-nostderr\fR
+No STDERR messages (only for the web server)
+.IP
+\- sequence order in pep.aln and nuc.fasta should be the same.
+.IP
+\- IDs in pep.aln are used in the output.
+.SH "SEE ALSO"
+The full documentation for
+.B pal2nal.pl
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B pal2nal.pl
+programs are properly installed at your site, the command
+.IP
+.B info pal2nal.pl
+.PP
+should give you access to the complete manual.
diff --git a/debian/pal2nal.install b/debian/pal2nal.install
new file mode 100644
index 0000000..a808529
--- /dev/null
+++ b/debian/pal2nal.install
@@ -0,0 +1 @@
+./pal2nal.pl /usr/bin
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..b760bee
--- /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
+
+%:
+ 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)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..2317f6a
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Mikita Suyama and David Torrents and Peer Bork
+ Title: "PAL2NAL: robust conversion of protein sequence alignment into the corresponding codon alignments"
+ Journal: Nucleic Acids Research
+ Year: 2006
+ Volume: 34
+ Pages: W609-W612
+ DOI: 10.1093/nar/gkl315
+ PMID: 16845082
+ URL: http://nar.oxfordjournals.org/content/34/suppl_2/W609
+ eprint: http://nar.oxfordjournals.org/content/34/suppl_2/W609.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..ad3fd9b
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+
+http://www.bork.embl.de/pal2nal/ distribution/pal2nal.v([.\d]+)\.tar\.gz
+
--
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