[med-svn] [pal2nal] 01/14: Added package for pal2nal. It seems to work, a few bits are pending, in particular there is no license for it, yet.

Sun Jan 15 10:12:18 UTC 2017

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tille pushed a commit to branch master
in repository pal2nal.

commit f61717498c0b78ee1dfd02b17c56984288b2be85
Author: Steffen Moeller <moeller at debian.org>
Date:   Tue Nov 23 15:37:36 2010 +0000

    Added package for pal2nal. It seems to work, a few bits are
    pending, in particular there is no license for it, yet.
---
 debian/README.Debian   |  7 +++++++
 debian/README.source   |  7 +++++++
 debian/changelog       |  5 +++++
 debian/compat          |  1 +
 debian/control         | 33 +++++++++++++++++++++++++++++++++
 debian/copyright       | 27 +++++++++++++++++++++++++++
 debian/docs            |  1 +
 debian/examples        |  2 ++
 debian/pal2nal.install |  1 +
 debian/rules           | 13 +++++++++++++
 debian/source/format   |  1 +
 11 files changed, 98 insertions(+)

diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..d5fef58
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,7 @@
+pal2nal for Debian
+------------------
+
+This package comes without a license and as such remains unredistributable
+untils this has been clarified with upstream.
+
+ -- Steffen Moeller <steffen_moeller at gmx.de>  Tue, 23 Nov 2010 16:18:36 +0100
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..02c3b5d
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,7 @@
+pal2nal for Debian
+------------------
+
+All source files where left intact,
+the name of the directory was changed
+to pal2nal-13, only.
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..48b167a
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+pal2nal (13-1) unstable; urgency=low
+
+  * Initial release (Closes: #nnnn)  <nnnn is the bug number of your ITP>
+
+ -- Steffen Moeller <steffen_moeller at gmx.de>  Tue, 23 Nov 2010 16:18:36 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..7f8f011
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+7
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..1699cf6
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,33 @@
+Source: pal2nal
+Section: science
+Priority: extra
+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>
+Build-Depends: debhelper (>= 7.0.50~)
+Standards-Version: 3.9.1
+Homepage: http://www.bork.embl.de/pal2nal
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/pal2nal/trunk
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/pal2nal/trunk/?rev=0&sc=0
+
+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.
+ .
+ If you use PAL2NAL, please cite the following paper:
+  Mikita Suyama, David Torrents, and Peer Bork (2006)
+  PAL2NAL: robust conversion of protein sequence alignment into
+  the corresponding codon alignments.
+  Nucleic Acids Res. 34:W609-W612.
+
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..67985a5
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,27 @@
+This work was packaged for Debian by:
+
+    Steffen Moeller <moeller at debian.org> on Tue, 23 Nov 2010 16:18:36 +0100
+
+It was downloaded from:
+
+    http://www.bork.embl.de/pal2nal/distribution/pal2nal.v13.tar.gz
+
+Upstream Authors:
+
+    Mikita Suyama <mikita at genome.med.kyoto-u.ac.jp>
+
+Copyright:
+
+    Copyright (C) 2006-2010 Mikita Suyama, David Torrents, and Peer Bork
+    and their respective employing institute.
+
+License:
+
+    <Put the license of the package here indented by 4 spaces>
+
+The Debian packaging is:
+
+    Copyright (C) 2010 Steffen Moeller <moeller at debian.org>
+
+and is licensed under the GPL version 3,
+see "/usr/share/common-licenses/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/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)

-- 
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