[med-svn] r12299 - in trunk/packages/zhanglab: . nw-align nw-align/trunk nw-align/trunk/debian nw-align/trunk/debian/source
Steffen Möller
moeller at alioth.debian.org
Sat Sep 29 16:38:52 UTC 2012
Author: moeller
Date: 2012-09-29 16:38:52 +0000 (Sat, 29 Sep 2012)
New Revision: 12299
Added:
trunk/packages/zhanglab/nw-align/
trunk/packages/zhanglab/nw-align/trunk/
trunk/packages/zhanglab/nw-align/trunk/debian/
trunk/packages/zhanglab/nw-align/trunk/debian/README.Debian
trunk/packages/zhanglab/nw-align/trunk/debian/README.source
trunk/packages/zhanglab/nw-align/trunk/debian/changelog
trunk/packages/zhanglab/nw-align/trunk/debian/compat
trunk/packages/zhanglab/nw-align/trunk/debian/control
trunk/packages/zhanglab/nw-align/trunk/debian/copyright
trunk/packages/zhanglab/nw-align/trunk/debian/docs
trunk/packages/zhanglab/nw-align/trunk/debian/nw-align.dirs
trunk/packages/zhanglab/nw-align/trunk/debian/nw-align.install
trunk/packages/zhanglab/nw-align/trunk/debian/rules
trunk/packages/zhanglab/nw-align/trunk/debian/source/
trunk/packages/zhanglab/nw-align/trunk/debian/source/format
Log:
nw-align is one of those tools that I packaged mostly for myself.
I am sharing the build instructions with the community here,
but I do not want to immediately maintain it. If someone feels like
adopting it - please go ahead. I happily perform as a sponsor.
The following issues are to be addressed prior to an upload:
W: nw-align source: newer-standards-version 3.9.4 (current is 3.9.3)
W: nw-align: hardening-no-relro usr/bin/nw-align
W: nw-align: hardening-no-fortify-functions usr/bin/nw-align
W: nw-align: wrong-bug-number-in-closes l3:#nnnn
W: nw-align: new-package-should-close-itp-bug
W: nw-align: binary-without-manpage usr/bin/nw-align
Cheers,
Steffen
Property changes on: trunk/packages/zhanglab/nw-align/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/zhanglab/nw-align/trunk/debian/README.Debian
===================================================================
--- trunk/packages/zhanglab/nw-align/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/zhanglab/nw-align/trunk/debian/README.Debian 2012-09-29 16:38:52 UTC (rev 12299)
@@ -0,0 +1,13 @@
+nw-align for Debian
+-------------------
+
+It is not completely clear to me if nw-align is ultimately required
+to be published. The Needleman-Wunsch global alignment is e.g. also
+implemented in EMBOSS, see
+http://emboss.sourceforge.net/apps/cvs/emboss/apps/needle.html
+
+However, this particular nw-align tool is part of the I-TASSER suite
+(named just 'align') and as such the one or other may find some
+particular affection for it.
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 29 Sep 2012 16:54:15 +0200
Added: trunk/packages/zhanglab/nw-align/trunk/debian/README.source
===================================================================
--- trunk/packages/zhanglab/nw-align/trunk/debian/README.source (rev 0)
+++ trunk/packages/zhanglab/nw-align/trunk/debian/README.source 2012-09-29 16:38:52 UTC (rev 12299)
@@ -0,0 +1,12 @@
+nw-align for Debian
+-------------------
+
+The .orig.tar.gz was manually assembled from information presented on
+http://zhanglab.ccmb.med.umich.edu/NW-align/
+namely the source code on
+http://zhanglab.ccmb.med.umich.edu/NW-align/NWalign.f
+and the BLAST matrix on
+http://zhanglab.ccmb.med.umich.edu/NW-align/BLOSUM62.txt
+
+
+
Added: trunk/packages/zhanglab/nw-align/trunk/debian/changelog
===================================================================
--- trunk/packages/zhanglab/nw-align/trunk/debian/changelog (rev 0)
+++ trunk/packages/zhanglab/nw-align/trunk/debian/changelog 2012-09-29 16:38:52 UTC (rev 12299)
@@ -0,0 +1,5 @@
+nw-align (0.20100803-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #nnnn)
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 29 Sep 2012 16:54:15 +0200
Added: trunk/packages/zhanglab/nw-align/trunk/debian/compat
===================================================================
--- trunk/packages/zhanglab/nw-align/trunk/debian/compat (rev 0)
+++ trunk/packages/zhanglab/nw-align/trunk/debian/compat 2012-09-29 16:38:52 UTC (rev 12299)
@@ -0,0 +1 @@
+8
Added: trunk/packages/zhanglab/nw-align/trunk/debian/control
===================================================================
--- trunk/packages/zhanglab/nw-align/trunk/debian/control (rev 0)
+++ trunk/packages/zhanglab/nw-align/trunk/debian/control 2012-09-29 16:38:52 UTC (rev 12299)
@@ -0,0 +1,19 @@
+Source: nw-align
+Section: science
+Priority: extra
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 8.0.0), gfortran
+Standards-Version: 3.9.4
+Homepage: http://zhanglab.ccmb.med.umich.edu/NW-align
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/nm-align/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/nm-align/trunk/
+
+Package: nw-align
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: emboss
+Description: global protein sequence alignment
+ NW-align is simple and robust alignment program for protein
+ sequence-to-sequence alignments based on the standard Needleman-Wunsch
+ dynamic programming algorithm. The implementation is performed in
+ FORTRAN.
Added: trunk/packages/zhanglab/nw-align/trunk/debian/copyright
===================================================================
--- trunk/packages/zhanglab/nw-align/trunk/debian/copyright (rev 0)
+++ trunk/packages/zhanglab/nw-align/trunk/debian/copyright 2012-09-29 16:38:52 UTC (rev 12299)
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: nw-align
+Source: http://zhanglab.ccmb.med.umich.edu/NW-align/
+
+Files: *
+Copyright: 2010 Yang Zhang <Email: zhng at umich.edu>
+License:
+ The program can be freely copied and modified provided the notices
+ on the head are retained. Comments and bug report should be addressed
+ to Yang Zhang (Email: zhng at umich.edu). Last update is in 2010/08/03.
+
+Files: debian/*
+Copyright: 2012 Steffen Moeller <moeller at debian.org>
+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 program. If not, see <http://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".
Added: trunk/packages/zhanglab/nw-align/trunk/debian/docs
===================================================================
--- trunk/packages/zhanglab/nw-align/trunk/debian/docs (rev 0)
+++ trunk/packages/zhanglab/nw-align/trunk/debian/docs 2012-09-29 16:38:52 UTC (rev 12299)
@@ -0,0 +1 @@
+BLOSUM62.txt
Added: trunk/packages/zhanglab/nw-align/trunk/debian/nw-align.dirs
===================================================================
--- trunk/packages/zhanglab/nw-align/trunk/debian/nw-align.dirs (rev 0)
+++ trunk/packages/zhanglab/nw-align/trunk/debian/nw-align.dirs 2012-09-29 16:38:52 UTC (rev 12299)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/zhanglab/nw-align/trunk/debian/nw-align.install
===================================================================
--- trunk/packages/zhanglab/nw-align/trunk/debian/nw-align.install (rev 0)
+++ trunk/packages/zhanglab/nw-align/trunk/debian/nw-align.install 2012-09-29 16:38:52 UTC (rev 12299)
@@ -0,0 +1 @@
+nw-align usr/bin
Added: trunk/packages/zhanglab/nw-align/trunk/debian/rules
===================================================================
--- trunk/packages/zhanglab/nw-align/trunk/debian/rules (rev 0)
+++ trunk/packages/zhanglab/nw-align/trunk/debian/rules 2012-09-29 16:38:52 UTC (rev 12299)
@@ -0,0 +1,23 @@
+#!/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 $@
+
+override_dh_auto_build:
+ gfortran -O3 -ffast-math -lm -o nw-align NWalign.f
+
+VERSION=0.20100803
+get-orig-source:
+ mkdir nw-align-$(VERSION)
+ cd nw-align-$(VERSION) && wget http://zhanglab.ccmb.med.umich.edu/NW-align/NWalign.f
+ cd nw-align-$(VERSION) && wget http://zhanglab.ccmb.med.umich.edu/NW-align/BLOSUM62.txt
+ GZIP=-9n tar cvf nw-align_$(VERSION).orig.tar.gz nw-align
Property changes on: trunk/packages/zhanglab/nw-align/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/zhanglab/nw-align/trunk/debian/source/format
===================================================================
--- trunk/packages/zhanglab/nw-align/trunk/debian/source/format (rev 0)
+++ trunk/packages/zhanglab/nw-align/trunk/debian/source/format 2012-09-29 16:38:52 UTC (rev 12299)
@@ -0,0 +1 @@
+3.0 (quilt)
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