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access;
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	TNF:1.1.1;
locks; strict;
comment	@# @;


1.5
date	2013.07.21.15.58.51;	author wen;	state Exp;
branches;
next	1.4;
commitid	xOIugSq8ytGVYlYw;

1.4
date	2009.07.08.15.20.04;	author joerg;	state Exp;
branches;
next	1.3;

1.3
date	2004.08.23.14.37.04;	author ben;	state Exp;
branches;
next	1.2;

1.2
date	2004.08.16.02.47.49;	author ben;	state Exp;
branches;
next	1.1;

1.1
date	2003.09.26.03.52.47;	author jschauma;	state Exp;
branches
	1.1.1.1;
next	;

1.1.1.1
date	2003.09.26.03.52.47;	author jschauma;	state Exp;
branches;
next	;


desc
@@


1.5
log
@Update to 3.0
Add LICENSE
Add more distfile mirrors

Upstream changelog please visit:
http://selab.janelia.org/software/hmmer3/3.0/RELEASE-NOTES
@
text
@$NetBSD: patch-aa,v 1.4 2009/07/08 15:20:04 joerg Exp $
replace "mkdir -p" with ${MKDIR} 
--- Makefile.in.orig	2013-07-21 23:25:33.000000000 +0000
+++ Makefile.in
@@@@ -51,7 +51,7 @@@@ CPPFLAGS  = @@CPPFLAGS@@
 
 # Other tools
 #
-INSTMAN   = cp
+INSTMAN   = ${BSD_INSTALL_MAN}
 AR        = @@AR@@ rcv
 LN        = ln
 RANLIB    = @@RANLIB@@
@@@@ -176,11 +176,11 @@@@ testsuite: libraries
 #          may be set on a make command line when building contrib RPMs).
 install: libraries programs
 	cd ${PMARKDIR}; ${MAKE} profmark_progs
-	-mkdir -p ${DESTDIR}${bindir}
+	-${MKDIR} ${DESTDIR}${bindir}
 	for file in $(PROGS); do\
-	   cp ${SRCDIR}/$$file ${DESTDIR}${bindir}/;\
+	   ${BSD_INSTALL_PROGRAM} ${SRCDIR}/$$file ${DESTDIR}${bindir}/;\
 	done
-#	-mkdir -p ${DESTDIR}/${MANDIR}/man${MANSUFFIX}
+#	-${MKDIR} ${DESTDIR}/${MANDIR}/man${MANSUFFIX}
 #	-for file in hmmer $(PROGS); do\
 #	   $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
 #	done
@


1.4
log
@user-destdir support
@
text
@d1 3
a3 3
$NetBSD$

--- Makefile.in.orig	2003-10-04 21:01:16.000000000 +0200
d5 1
a5 5
@@@@ -30,11 +30,12 @@@@ prefix      = @@prefix@@
 exec_prefix = @@exec_prefix@@
 BINDIR      = @@bindir@@
 MANDIR      = @@mandir@@
+INSTBIN     = ${BSD_INSTALL_PROGRAM}
d7 1
a7 2
 # how to install the man pages; 
 # cp is generally fine, unless you preformat your pages.
d11 12
a22 29
 MANSUFFIX = 1
 
 # your compiler and compiler flags
@@@@ -109,13 +110,13 @@@@ src/libhmmer.a: 
 #          installs man pages in MANDIR/man1/  (e.g. if MANSUFFIX is 1)
 #          Creates these directories if they don't exist.
 install: 
-	mkdir -p ${BINDIR}
-	-mkdir -p ${MANDIR}/man${MANSUFFIX}
+	${MKDIR} ${DESTDIR}${BINDIR}
+	-${MKDIR} ${DESTDIR}${MANDIR}/man${MANSUFFIX}
 	for file in $(PROGS) $(PVMPROGS); do\
-	   cp src/$$file $(BINDIR)/;\
+	   $(INSTBIN) src/$$file ${DESTDIR}$(BINDIR)/;\
 	done
 	-for file in hmmer $(PROGS); do\
-	   $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+	   $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
 	done
 
 # uninstall: Reverses the steps of "make install".
@@@@ -133,7 +134,7 @@@@ uninstall: 
 #          subdir, remove everything but binaries and Makefiles.
 #
 bindist:
-	mkdir binaries
+	${MKDIR} binaries
 	for prog in $(PROGS); do\
 	   (cd binaries; ln -s ../src/$$prog .);\
d24 5
a28 18
@@@@ -205,7 +206,7 @@@@ dist:	
 	# in testsuite. 
 	#
 	cp ssdk/sqc ${BASENAME}-${RELEASE}/testsuite/
-	mkdir ${BASENAME}-${RELEASE}/ssdk
+	${MKDIR} ${BASENAME}-${RELEASE}/ssdk
 	cp ssdk/rmanprocess.pl ${BASENAME}-${RELEASE}/ssdk/
 	# 
 	# Make the configure scripts from configure.ac
@@@@ -288,7 +289,7 @@@@ dist:	
 #               directory.
 #
 ftpdist:
-	mkdir -p ${FTPDIR}
+	${MKDIR} ${FTPDIR}
 	cp -f hmmer-$(RELEASE)/00README         ${FTPDIR}
 	cp -f hmmer-$(RELEASE)/COPYRIGHT        ${FTPDIR}
 	cp -f hmmer-$(RELEASE)/INSTALL          ${FTPDIR}
@


1.3
log
@Remove unnecessary -p following MKDIR commands.
@
text
@d1 1
a1 1
$NetBSD: patch-aa,v 1.2 2004/08/16 02:47:49 ben Exp $
d3 1
a3 1
--- Makefile.in.orig	Fri Jun 13 14:05:13 2003
d19 1
a19 1
@@@@ -109,10 +110,10 @@@@ src/libhmmer.a: 
d25 2
a26 2
+	${MKDIR} ${BINDIR}
+	-${MKDIR} ${MANDIR}/man${MANSUFFIX}
d29 1
a29 1
+	   $(INSTBIN) src/$$file $(BINDIR)/;\
d32 5
a36 1
 	   $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
d55 1
a55 1
@@@@ -293,7 +294,7 @@@@ dist:	
@


1.2
log
@Make hmmer honor $MKDIR for cross-platform install.
Addresses pr#26650 from Georg Schwarz.
@
text
@d1 1
a1 1
$NetBSD$
d25 2
a26 2
+	${MKDIR} -p ${BINDIR}
+	-${MKDIR} -p ${MANDIR}/man${MANSUFFIX}
d56 1
a56 1
+	${MKDIR} -p ${FTPDIR}
@


1.1
log
@Initial revision
@
text
@d1 1
a1 1
$NetBSD: $
d3 3
a5 3
--- Makefile.in.orig	2003-06-13 17:05:13.000000000 -0400
+++ Makefile.in	2003-09-25 23:47:27.000000000 -0400
@@@@ -30,11 +30,12 @@@@
d19 8
a26 3
@@@@ -112,7 +113,7 @@@@
 	mkdir -p ${BINDIR}
 	-mkdir -p ${MANDIR}/man${MANSUFFIX}
d33 27
@


1.1.1.1
log
@Initial import of hmmer,  one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

HMMER is an implementation of profile HMM methods for sensitive database 
searches using multiple sequence alignments as queries. HMMER takes 
multiple sequence alignement as input and builds statistical model 
called "Hidden Markov Model" which can be used as a query into a 
sequence database to find and/or align additional homologues of the 
sequence family.
@
text
@@