[med-svn] r1689 - in trunk/packages/clustalw-mpi/trunk: . debian debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Mon Apr 7 06:28:53 UTC 2008
Author: tille
Date: 2008-04-07 06:28:52 +0000 (Mon, 07 Apr 2008)
New Revision: 1689
Added:
trunk/packages/clustalw-mpi/trunk/debian/clustalw-mpi.1
trunk/packages/clustalw-mpi/trunk/debian/manpages
trunk/packages/clustalw-mpi/trunk/debian/patches/
trunk/packages/clustalw-mpi/trunk/debian/patches/01_Makefile.patch
trunk/packages/clustalw-mpi/trunk/debian/patches/series
Removed:
trunk/packages/clustalw-mpi/trunk/Makefile
trunk/packages/clustalw-mpi/trunk/clustalw-mpi.1
trunk/packages/clustalw-mpi/trunk/debian/t.sh
trunk/packages/clustalw-mpi/trunk/t.sh
Modified:
trunk/packages/clustalw-mpi/trunk/debian/changelog
trunk/packages/clustalw-mpi/trunk/debian/compat
trunk/packages/clustalw-mpi/trunk/debian/control
trunk/packages/clustalw-mpi/trunk/debian/copyright
trunk/packages/clustalw-mpi/trunk/debian/rules
Log:
Group maintenance for clustalw-mpi
Deleted: trunk/packages/clustalw-mpi/trunk/Makefile
===================================================================
--- trunk/packages/clustalw-mpi/trunk/Makefile 2008-04-06 03:57:19 UTC (rev 1688)
+++ trunk/packages/clustalw-mpi/trunk/Makefile 2008-04-07 06:28:52 UTC (rev 1689)
@@ -1,78 +0,0 @@
-
-DESTDIR = /usr/local
-DOCDIR = $(DESTDIR)/usr/share/doc/clustalw-mpi
-BINDIR = $(DESTDIR)/usr/bin
-MANDIR = $(DESTDIR)/usr/share/man/man1
-DOCS = README.clustalw-mpi dele.input
-BINS = clustalw-mpi
-
-RM = /bin/rm -f
-
-OBJECTS = clustalw-mpi.o interface.o sequence.o showpair.o malign.o malign_mpi_progressive.o \
- malign_mpi_pdiff.o util.o trees.o gcgcheck.o \
- prfalign_mpi_pdiff.o prfalign_mpi_progressive.o pairalign_new.o \
- calcgapcoeff.o calcprf1.o calcprf2.o calctree.o \
- readmat.o alnscore.o random.o parallel_compare.o \
- prfalign.o stupid.o
-
-HEADERS = general.h clustalw.h
-
-CC = mpicc
-
-TREES_FLAG = -DSERIAL_NJTREE
-
-#
-# Choose either dynamic or static scheduling for pairalign():
-# the default is to use dynamic scheduling. You might also
-# want to check PAIRALIGN_NCHUNK in clustalw.h. The
-# larger this marco, the smaller the chunk size, default is 100.
-#
-PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN
-#PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN
-
-CFLAGS = -O3
-#CFLAGS = -O3 -funroll-all-loops
-LFLAGS = -lm
-
-all: clustalw-mpi
-
-install: all
- install -d $(BINDIR) $(DOCDIR) $(MANDIR)
- install -m 755 clustalw-mpi $(BINDIR)
- install -m 644 $(DOCS) $(DOCDIR)
- install -m 0644 clustalw-mpi.1 $(MANDIR)
-
-
-
-clustalw-mpi: $(OBJECTS)
- $(CC) -o $@ $(OBJECTS) $(LFLAGS)
-
-interface.o : interface.c $(HEADERS) param.h
- $(CC) -c $(CFLAGS) $*.c
-
-readmat.o : readmat.c $(HEADERS) matrices.h
- $(CC) -c $(CFLAGS) $*.c
-
-trees.o : trees.c $(HEADERS) dayhoff.h
- $(CC) -c $(TREES_FLAG) $(CFLAGS) $*.c
-
-pairalign_new.o : pairalign_new.c $(HEADERS)
- $(CC) -c $(PAIRALIGN_FLAG) $(CFLAGS) $*.c
-parallel_compare.o : parallel_compare.c $(HEADERS) dayhoff.h
- $(CC) -c $(PAIRALIGN_FLAG) $(CFLAGS) $*.c
-
-
-.PHONY: clean distclean
-
-.SUFFIXES: .c .o
-
-
-.c.o :
- $(CC) -c $(CFLAGS) $?
-
-
-clean:
- $(RM) -f *.o
-
-distclean: clean
- $(RM) $(BINS)
Deleted: trunk/packages/clustalw-mpi/trunk/clustalw-mpi.1
===================================================================
--- trunk/packages/clustalw-mpi/trunk/clustalw-mpi.1 2008-04-06 03:57:19 UTC (rev 1688)
+++ trunk/packages/clustalw-mpi/trunk/clustalw-mpi.1 2008-04-07 06:28:52 UTC (rev 1689)
@@ -1,43 +0,0 @@
-.\"
-.\" The man page was derived from the man page of Chet Ramey for the BASH
-.\"
-
-.TH CLUSTALW\-MPI 1 "2003\ April\ 8" "ClustalW\-MPI 0.13"
-
-.SH NAME
-ClustalW-MPI \- MPI distributed ClustalW
-
-.SH SYNOPSIS
-mpirun [\fImpirun_options\fR] clustalw-mpi [\fIclustalw options\fR]
-
-.SH DESCRIPTION
-.B ClustalW-MPI
-is an MPI implementation of ClustalW. It utilizes your networked computers to
-globally align sets of nucleic or amino acid sequences.
-
-.SH EXAMPLES
-To make a full multiple sequence alignment (using one master node and 4 computing nodes):
-
-mpirun -np 5 ./clustalw-mpi -infile=dele.input
-
-
-To make a guide tree only:
-
-mpirun -np 5 ./clustalw-mpi -infile=dele.input -newtree=dele.mytree
-
-
-To make a multiple sequence alignment out of an existing tree:
-
-mpirun -np 5 ./clustalw-mpi -infile=dele.input -usetree=dele.mytree
-
-.SH COPYRIGHT
-.if n clutalw-mpi is Copyright (C) 2003 by Dr. Kuo-Bin Li, Bioinformatics Institute, Singapure
-.if t clutalw-mpi is Copyright \(co 2003 by Dr. Kuo-Bin Li, Bioinformatics Institute, Singapure
-
-.SH OPTIONS
-See man page for clustalw.
-.SH SEE ALSO
-.B clustalw
-(1)
-.SH AUTHORS
-Dr. Kuo-Bin Li <kuobin at bii.a-star.edu.sg>, Bioinformatics Institute, Singapore.
Modified: trunk/packages/clustalw-mpi/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/changelog 2008-04-06 03:57:19 UTC (rev 1688)
+++ trunk/packages/clustalw-mpi/trunk/debian/changelog 2008-04-07 06:28:52 UTC (rev 1689)
@@ -1,3 +1,20 @@
+clustalw-mpi (0.13-4) unstable; urgency=low
+
+ * Put package under group maintenance of Debian-Med Team
+ - XS-DM-Upload-Allowed: Yes
+ - Vcs tags
+ - Use correct address as Uploader: Steffen Moeller <moeller at debian.org>
+ * Switched to quilt
+ - Move manpage to debian dri and added debian/manpages
+ - Patched Makefile accordingly
+ - removed useless t.sh
+ * Standards-Version: 3.7.3 (no changes needed)
+ * debhelper >= 5
+ * Moved Homepage from long description to control fields
+ * debian/copyright machine readable
+
+ -- Andreas Tille <tille at debian.org> Sun, 06 Apr 2008 20:23:04 +0200
+
clustalw-mpi (0.13-3) unstable; urgency=low
* Updated lam4 to 7.1.1 (Closes: Bug#329488)
Added: trunk/packages/clustalw-mpi/trunk/debian/clustalw-mpi.1
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/clustalw-mpi.1 (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/clustalw-mpi.1 2008-04-07 06:28:52 UTC (rev 1689)
@@ -0,0 +1,43 @@
+.\"
+.\" The man page was derived from the man page of Chet Ramey for the BASH
+.\"
+
+.TH CLUSTALW\-MPI 1 "2003\ April\ 8" "ClustalW\-MPI 0.13"
+
+.SH NAME
+ClustalW-MPI \- MPI distributed ClustalW
+
+.SH SYNOPSIS
+mpirun [\fImpirun_options\fR] clustalw-mpi [\fIclustalw options\fR]
+
+.SH DESCRIPTION
+.B ClustalW-MPI
+is an MPI implementation of ClustalW. It utilizes your networked computers to
+globally align sets of nucleic or amino acid sequences.
+
+.SH EXAMPLES
+To make a full multiple sequence alignment (using one master node and 4 computing nodes):
+
+mpirun -np 5 ./clustalw-mpi -infile=dele.input
+
+
+To make a guide tree only:
+
+mpirun -np 5 ./clustalw-mpi -infile=dele.input -newtree=dele.mytree
+
+
+To make a multiple sequence alignment out of an existing tree:
+
+mpirun -np 5 ./clustalw-mpi -infile=dele.input -usetree=dele.mytree
+
+.SH COPYRIGHT
+.if n clutalw-mpi is Copyright (C) 2003 by Dr. Kuo-Bin Li, Bioinformatics Institute, Singapure
+.if t clutalw-mpi is Copyright \(co 2003 by Dr. Kuo-Bin Li, Bioinformatics Institute, Singapure
+
+.SH OPTIONS
+See man page for clustalw.
+.SH SEE ALSO
+.B clustalw
+(1)
+.SH AUTHORS
+Dr. Kuo-Bin Li <kuobin at bii.a-star.edu.sg>, Bioinformatics Institute, Singapore.
Modified: trunk/packages/clustalw-mpi/trunk/debian/compat
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/compat 2008-04-06 03:57:19 UTC (rev 1688)
+++ trunk/packages/clustalw-mpi/trunk/debian/compat 2008-04-07 06:28:52 UTC (rev 1689)
@@ -1 +1 @@
-4
+5
Modified: trunk/packages/clustalw-mpi/trunk/debian/control
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/control 2008-04-06 03:57:19 UTC (rev 1688)
+++ trunk/packages/clustalw-mpi/trunk/debian/control 2008-04-07 06:28:52 UTC (rev 1689)
@@ -1,10 +1,15 @@
Source: clustalw-mpi
Section: non-free/science
Priority: optional
-Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
-Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>> 4.0.0), lam4-dev (>= 7.1.1-3.2)
-Standards-Version: 3.5.10
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+XS-DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 4.0), lam4-dev (>= 7.1.1-3.2), quilt
+Standards-Version: 3.7.3
+Homepage: http://www.bii.a-star.edu.sg/~kuobin/clustalw-mpi/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/clustalw-mpi/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/clustalw-mpi/trunk/
Package: clustalw-mpi
Architecture: any
@@ -36,5 +41,3 @@
.
The original ClustalW/ClustalX can be found at
URL: ftp://ftp-igbmc.u-strasbg.fr
- .
- Homepage: http://www.bii.a-star.edu.sg/~kuobin/clustalw-mpi/
Modified: trunk/packages/clustalw-mpi/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/copyright 2008-04-06 03:57:19 UTC (rev 1688)
+++ trunk/packages/clustalw-mpi/trunk/debian/copyright 2008-04-07 06:28:52 UTC (rev 1689)
@@ -1,15 +1,20 @@
-This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
-Mon, 30 Jun 2003 22:54:41 +0200.
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>
+X-Debianized-Date: Mon, 30 Jun 2003 22:54:41 +0200.
+X-Source-Downloaded-From: http://www.bii.a-star.edu.sg/~kuobin/clustalg/clustalw-mpi-0.13.tar.gz
+X-Upstream-Author: Dr. Kuo-Bin Li <kuobin at bii.a-star.edu.sg>
-It was downloaded from http://www.bii.a-star.edu.sg/~kuobin/clustalg/clustalw-mpi-0.13.tar.gz
+Files: debian/*
+Copyright: © 2003—2008 Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>
+License: GPL-2+
+X-Comment: On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL'.
-Upstream Author: Dr. Kuo-Bin Li <kuobin at bii.a-star.edu.sg>
-
-Copyright:
- Dr. Kuo-Bin Li, Bioinformatics Institute, Singapore
- .
- COPYRIGHT and LICENSING POLICY
- .
+Files: *
+Copyright: © 2001-2003 Dr. Kuo-Bin Li, Bioinformatics Institute, Singapore
+License: COPYRIGHT and LICENSING POLICY
CLUSTALW-MPI is freely available to the user community. You can
redistribute it and/or modify it. Since CLUSTALW-MPI was derived from
CLUSTAL W, the original license policy of CLUSTAL W is listed here:
@@ -20,8 +25,3 @@
distributors of Clustal W must take out a NON-EXCLUSIVE LICENCE. Anyone
wishing to commercially distribute version 1.81 of Clustal W should contact the
authors unless they have previously taken out a licence.
-
-
-
-
-
Added: trunk/packages/clustalw-mpi/trunk/debian/manpages
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/manpages (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/manpages 2008-04-07 06:28:52 UTC (rev 1689)
@@ -0,0 +1 @@
+debian/clustalw-mpi.1
Added: trunk/packages/clustalw-mpi/trunk/debian/patches/01_Makefile.patch
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/patches/01_Makefile.patch (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/patches/01_Makefile.patch 2008-04-07 06:28:52 UTC (rev 1689)
@@ -0,0 +1,73 @@
+--- clustalw-mpi-0.13.orig/Makefile
++++ clustalw-mpi-0.13/Makefile
+@@ -1,7 +1,13 @@
+-install: clustalw-mpi
++#!/usr/bin/make
+
+-clean:
+- /bin/rm -f *.o
++DESTDIR = /usr/local
++DOCDIR = $(DESTDIR)/usr/share/doc/clustalw-mpi
++BINDIR = $(DESTDIR)/usr/bin
++MANDIR = $(DESTDIR)/usr/share/man/man1
++DOCS = README.clustalw-mpi dele.input
++BINS = clustalw-mpi
++
++RM = /bin/rm -f
+
+ OBJECTS = clustalw-mpi.o interface.o sequence.o showpair.o malign.o malign_mpi_progressive.o \
+ malign_mpi_pdiff.o util.o trees.o gcgcheck.o \
+@@ -25,29 +31,45 @@
+ PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN
+ #PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN
+
+-CFLAGS = -c -O3
+-#CFLAGS = -c -O3 -funroll-all-loops
++CFLAGS = -O3
++#CFLAGS = -O3 -funroll-all-loops
+ LFLAGS = -lm
+
++all: clustalw-mpi
++
++install: all
++ install -d $(BINDIR) $(DOCDIR) $(MANDIR)
++ install -m 755 clustalw-mpi $(BINDIR)
++ install -m 644 $(DOCS) $(DOCDIR)
++
+ clustalw-mpi: $(OBJECTS)
+ $(CC) -o $@ $(OBJECTS) $(LFLAGS)
+
+ interface.o : interface.c $(HEADERS) param.h
+- $(CC) $(CFLAGS) $*.c
++ $(CC) -c $(CFLAGS) $*.c
+
+ readmat.o : readmat.c $(HEADERS) matrices.h
+- $(CC) $(CFLAGS) $*.c
++ $(CC) -c $(CFLAGS) $*.c
+
+ trees.o : trees.c $(HEADERS) dayhoff.h
+- $(CC) $(TREES_FLAG) $(CFLAGS) $*.c
++ $(CC) -c $(TREES_FLAG) $(CFLAGS) $*.c
+
+ pairalign_new.o : pairalign_new.c $(HEADERS)
+- $(CC) $(PAIRALIGN_FLAG) $(CFLAGS) $*.c
++ $(CC) -c $(PAIRALIGN_FLAG) $(CFLAGS) $*.c
+ parallel_compare.o : parallel_compare.c $(HEADERS) dayhoff.h
+- $(CC) $(PAIRALIGN_FLAG) $(CFLAGS) $*.c
++ $(CC) -c $(PAIRALIGN_FLAG) $(CFLAGS) $*.c
+
++.PHONY: clean distclean
++
++.SUFFIXES: .c .o
+
+
+ .c.o :
+- $(CC) $(CFLAGS) $?
++ $(CC) -c $(CFLAGS) $?
++
++
++clean:
++ $(RM) -f *.o
+
++distclean: clean
++ $(RM) $(BINS)
Added: trunk/packages/clustalw-mpi/trunk/debian/patches/series
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/patches/series (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/patches/series 2008-04-07 06:28:52 UTC (rev 1689)
@@ -0,0 +1 @@
+01_Makefile.patch
Modified: trunk/packages/clustalw-mpi/trunk/debian/rules
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/rules 2008-04-06 03:57:19 UTC (rev 1688)
+++ trunk/packages/clustalw-mpi/trunk/debian/rules 2008-04-07 06:28:52 UTC (rev 1689)
@@ -1,10 +1,13 @@
#!/usr/bin/make -f
-# Sample debian/rules that uses debhelper.
-# GNU copyright 1997 to 1999 by Joey Hess.
+# debian/rules for clustalw-mpi
+# Copyright 2004-2008 Steffen Moeller, Andreas Tille
+# GPL
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
+include /usr/share/quilt/quilt.make
+
CFLAGS = -Wall -g
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
@@ -22,20 +25,23 @@
touch configure-stamp
-build: build-stamp
+build: patch build-stamp
build-stamp: configure-stamp
dh_testdir
$(MAKE)
touch build-stamp
-clean:
+clean-patched:
dh_testdir
dh_testroot
rm -f build-stamp configure-stamp
- -$(MAKE) distclean
+ # Try only distclean if we are working on the patched source
+ if grep -q distclean Makefile ; then $(MAKE) distclean ; fi
dh_clean
+clean: clean-patched unpatch
+
install: build
dh_testdir
dh_testroot
Deleted: trunk/packages/clustalw-mpi/trunk/debian/t.sh
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/t.sh 2008-04-06 03:57:19 UTC (rev 1688)
+++ trunk/packages/clustalw-mpi/trunk/debian/t.sh 2008-04-07 06:28:52 UTC (rev 1689)
@@ -1,2 +0,0 @@
-#!/bin/sh
-echo huhu
Deleted: trunk/packages/clustalw-mpi/trunk/t.sh
===================================================================
--- trunk/packages/clustalw-mpi/trunk/t.sh 2008-04-06 03:57:19 UTC (rev 1688)
+++ trunk/packages/clustalw-mpi/trunk/t.sh 2008-04-07 06:28:52 UTC (rev 1689)
@@ -1,2 +0,0 @@
-#!/bin/sh
-echo huhu
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