[med-svn] r1394 - in trunk/packages/clustalw-mpi/trunk: . debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sat Feb 16 01:37:18 UTC 2008
Author: charles-guest
Date: 2008-02-16 01:37:18 +0000 (Sat, 16 Feb 2008)
New Revision: 1394
Added:
trunk/packages/clustalw-mpi/trunk/clustalw-mpi.1
trunk/packages/clustalw-mpi/trunk/debian/
trunk/packages/clustalw-mpi/trunk/debian/README.Debian
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/dirs
trunk/packages/clustalw-mpi/trunk/debian/docs
trunk/packages/clustalw-mpi/trunk/debian/rules
trunk/packages/clustalw-mpi/trunk/debian/t.sh
trunk/packages/clustalw-mpi/trunk/t.sh
Modified:
trunk/packages/clustalw-mpi/trunk/Makefile
Log:
[svn-inject] Applying Debian modifications to trunk
Modified: trunk/packages/clustalw-mpi/trunk/Makefile
===================================================================
--- trunk/packages/clustalw-mpi/trunk/Makefile 2008-02-16 01:36:58 UTC (rev 1393)
+++ trunk/packages/clustalw-mpi/trunk/Makefile 2008-02-16 01:37:18 UTC (rev 1394)
@@ -1,8 +1,13 @@
-install: clustalw-mpi
-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 \
prfalign_mpi_pdiff.o prfalign_mpi_progressive.o pairalign_new.o \
@@ -25,29 +30,49 @@
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)
+ install -m 0644 clustalw-mpi.1 $(MANDIR)
+
+
+
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/clustalw-mpi.1
===================================================================
--- trunk/packages/clustalw-mpi/trunk/clustalw-mpi.1 (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/clustalw-mpi.1 2008-02-16 01:37:18 UTC (rev 1394)
@@ -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.
Property changes on: trunk/packages/clustalw-mpi/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/clustalw-mpi/trunk/debian/README.Debian
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/README.Debian 2008-02-16 01:37:18 UTC (rev 1394)
@@ -0,0 +1,8 @@
+clustalw-mpi for Debian
+-----------------------
+
+ * ClustalW-MPI shares code with ClustalW. The latter had to go into non-free since
+ its commercial redistribution is not allowed. Hence, this is also where its MPI
+ extension goes.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Mon, 30 Jun 2003 22:54:41 +0200
Added: trunk/packages/clustalw-mpi/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/changelog (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/changelog 2008-02-16 01:37:18 UTC (rev 1394)
@@ -0,0 +1,22 @@
+clustalw-mpi (0.13-3) unstable; urgency=low
+
+ * Updated lam4 to 7.1.1 (Closes: Bug#329488)
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 12 Oct 2005 15:07:41 +0200
+
+clustalw-mpi (0.13-2) unstable; urgency=low
+
+ * Updated lam3 to lam4 (Closes: #229939)
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Mon, 30 Jun 2003 22:54:41 +0200
+
+clustalw-mpi (0.13-1) unstable; urgency=low
+
+ * Initial Release. (Closes: #199837)
+ * Upstream author was very supportive
+ - provided man page
+ - provided license information
+ * Minimal changes to the makefile
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Mon, 30 Jun 2003 22:54:41 +0200
+
Added: trunk/packages/clustalw-mpi/trunk/debian/compat
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/compat (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/compat 2008-02-16 01:37:18 UTC (rev 1394)
@@ -0,0 +1 @@
+4
Added: trunk/packages/clustalw-mpi/trunk/debian/control
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/control (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/control 2008-02-16 01:37:18 UTC (rev 1394)
@@ -0,0 +1,40 @@
+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
+
+Package: clustalw-mpi
+Architecture: any
+Enhances: clustalw
+Suggests: seaview, clustalx
+Depends: ${shlibs:Depends}, lam-runtime (>= 7.1.1)
+Description: [Biology] MPI-distributed global sequence alignment with ClustalW
+ ClustalW is a popular tool for multiple sequence alignment. The
+ alignment is achieved via three steps: pairwise alignment,
+ guide-tree generation and progressive alignment. ClustalW-MPI is an
+ MPI implementation of ClustalW. Based on
+ version 1.82 of the original ClustalW, both the pairwise
+ and progressive alignments are parallelized with MPI, a
+ popular message passing programming standard. The
+ pairwise alignments can be easily parallelized since the many
+ alignments are time independent on each other. However
+ the progressive alignments are essentially not parallelizable
+ because of the time dependencies between each alignment.
+ .
+ Here the recursive parallelism paradigm is applied to the linear space
+ profile-profile alignment algorithm. This approach is more time
+ efficient on computers with distributed memory architecture.
+ Traditional approach that relies on precomputing the profile-profile
+ score matrix has also been implemented. Results shown the latter is indeed
+ more appropriate for shared memory multiprocessor computer.
+ .
+ ClustalX is suggested for its support for local realignments, seaview
+ is a versatile editor of alignments.
+ .
+ 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/
Added: trunk/packages/clustalw-mpi/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/copyright (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/copyright 2008-02-16 01:37:18 UTC (rev 1394)
@@ -0,0 +1,27 @@
+This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
+Mon, 30 Jun 2003 22:54:41 +0200.
+
+It was downloaded from http://www.bii.a-star.edu.sg/~kuobin/clustalg/clustalw-mpi-0.13.tar.gz
+
+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
+ .
+ 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:
+ .
+ Clustal W is freely available to the user community. However, Clustal W is
+ increasingly being distributed as part of commercial sequence analysis
+ packages. To help us safeguard future maintenance and development, commercial
+ 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/dirs
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/dirs (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/dirs 2008-02-16 01:37:18 UTC (rev 1394)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/clustalw-mpi/trunk/debian/docs
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/docs (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/docs 2008-02-16 01:37:18 UTC (rev 1394)
@@ -0,0 +1 @@
+README.clustalw-mpi
Added: trunk/packages/clustalw-mpi/trunk/debian/rules
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/rules (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/rules 2008-02-16 01:37:18 UTC (rev 1394)
@@ -0,0 +1,76 @@
+#!/usr/bin/make -f
+# Sample debian/rules that uses debhelper.
+# GNU copyright 1997 to 1999 by Joey Hess.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
+ INSTALL_PROGRAM += -s
+endif
+
+configure: configure-stamp
+configure-stamp:
+ dh_testdir
+ touch configure-stamp
+
+
+build: build-stamp
+
+build-stamp: configure-stamp
+ dh_testdir
+ $(MAKE)
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+ -$(MAKE) distclean
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+ $(MAKE) install DESTDIR=$(CURDIR)/debian/clustalw-mpi
+
+
+binary-indep: build install
+
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples
+# dh_install
+# dh_installmenu
+# dh_installdebconf
+# dh_installmime
+# dh_installinit
+# dh_installinfo
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+get-orig-source:
+ wget http://www.bii.a-star.edu.sg/~kuobin/clustalg/clustalw-mpi-0.13.tar.gz && mv clustalw-mpi-0.13.tar.gz clustalw-mpi_0.13.orig.tar.gz
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure get-orig-source
Property changes on: trunk/packages/clustalw-mpi/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/clustalw-mpi/trunk/debian/t.sh
===================================================================
--- trunk/packages/clustalw-mpi/trunk/debian/t.sh (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/debian/t.sh 2008-02-16 01:37:18 UTC (rev 1394)
@@ -0,0 +1,2 @@
+#!/bin/sh
+echo huhu
Added: trunk/packages/clustalw-mpi/trunk/t.sh
===================================================================
--- trunk/packages/clustalw-mpi/trunk/t.sh (rev 0)
+++ trunk/packages/clustalw-mpi/trunk/t.sh 2008-02-16 01:37:18 UTC (rev 1394)
@@ -0,0 +1,2 @@
+#!/bin/sh
+echo huhu
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