Mechanical changes to add full DESTDIR support to packages that install

their files via a custom do-install target.

16 files changed, 128 insertions, 87 deletions

diff --git a/biology/arka/Makefile b/biology/arka/Makefile
index 940aed6fe9f..95d44e455c5 100644
--- a/biology/arka/Makefile
+++ b/biology/arka/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.7 2007/02/22 19:26:09 wiz Exp $
+# $NetBSD: Makefile,v 1.8 2008/03/03 01:10:05 jlam Exp $
 #
 
 DISTNAME=	arka-0.11
@@ -13,6 +13,8 @@ COMMENT=	Graphic interface for the programs from the GP package
 
 DEPENDS+=	gp-[0-9]*:../../biology/gp
 
+PKG_DESTDIR_SUPPORT=	user-destdir
+
 USE_DIRS+=	xdg-1.1
 
 CONF_FILES=	${PREFIX}/share/examples/arka/arkarc ${PKG_SYSCONFDIR}/arkarc
@@ -26,17 +28,17 @@ post-build:
 	cd ${WRKSRC} && ${GUNZIP_CMD} arka.1.gz
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/arka ${PREFIX}/bin
-	${INSTALL_MAN} ${WRKSRC}/arka.1 ${PREFIX}/${PKGMANDIR}/man1
+	${INSTALL_PROGRAM} ${WRKSRC}/arka ${DESTDIR}${PREFIX}/bin
+	${INSTALL_MAN} ${WRKSRC}/arka.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
 .for f in arka_16x16.xpm arka_32x32.xpm
-	${INSTALL_DATA} ${WRKSRC}/icons/${f} ${PREFIX}/share/pixmaps
+	${INSTALL_DATA} ${WRKSRC}/icons/${f} ${DESTDIR}${PREFIX}/share/pixmaps
 .endfor
-	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/arka
+	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/arka
 .for f in CHANGES.TXT INSTALL.TXT LICENSE.TXT README.TXT TODO.TXT
-	${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/share/doc/arka
+	${INSTALL_DATA} ${WRKSRC}/${f} ${DESTDIR}${PREFIX}/share/doc/arka
 .endfor
-	${INSTALL_DATA_DIR} ${PREFIX}/share/examples/arka
-	${INSTALL_DATA} ${WRKSRC}/arkarc ${PREFIX}/share/examples/arka
+	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/examples/arka
+	${INSTALL_DATA} ${WRKSRC}/arkarc ${DESTDIR}${PREFIX}/share/examples/arka
 
 .include "../../x11/gtk/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/azara/Makefile b/biology/azara/Makefile
index 9b324e0777a..5b4310f276e 100644
--- a/biology/azara/Makefile
+++ b/biology/azara/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.5 2007/01/26 22:05:14 joerg Exp $
+# $NetBSD: Makefile,v 1.6 2008/03/03 01:10:05 jlam Exp $
 #
 
 DISTNAME=		azara-2.7-src
@@ -11,10 +11,13 @@ MAINTAINER=		mchittur@cs.nmsu.edu
 HOMEPAGE=		http://www.bio.cam.ac.uk/azara/
 COMMENT=		Programs to process and view NMR data
 
-WRKSRC=			${WRKDIR}/azara-2.7
+PKG_DESTDIR_SUPPORT=	user-destdir
 
+WRKSRC=			${WRKDIR}/azara-2.7
 MAKE_FILE=		makefile
 
+INSTALLATION_DIRS=	bin
+
 do-install:
 .for PROG in azara \
 		bin2asc \
@@ -29,7 +32,7 @@ do-install:
 		reflate \
 		slides swap \
 		unblock viewer
-		${CP} ${WRKSRC}/bin/${PROG} ${PREFIX}/bin
+		${CP} ${WRKSRC}/bin/${PROG} ${DESTDIR}${PREFIX}/bin
 .endfor
 
 .include "../../graphics/glu/buildlink3.mk"
diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile
index 4e5c6551a91..220ee238e19 100644
--- a/biology/clustalw/Makefile
+++ b/biology/clustalw/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.10 2006/10/04 20:47:03 wiz Exp $
+# $NetBSD: Makefile,v 1.11 2008/03/03 01:10:05 jlam Exp $
 
 DISTNAME=	clustalw1.83.UNIX
 PKGNAME=	clustalw-1.83
@@ -11,6 +11,7 @@ HOMEPAGE=	http://bips.u-strasbg.fr/fr/Documentation/ClustalW/
 COMMENT=	General purpose multiple alignment program for DNA or proteins
 
 PKG_INSTALLATION_TYPES=	overwrite pkgviews
+PKG_DESTDIR_SUPPORT=	user-destdir
 
 MAKE_FILE=	makefile
 BUILD_TARGET=	clustalw
@@ -26,10 +27,11 @@ post-patch:
 		&& ${MV} ${WRKSRC}/clustalw.c.tmp ${WRKSRC}/clustalw.c
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${PREFIX}/bin
-	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/clustalw
+	${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${DESTDIR}${PREFIX}/bin
+	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/clustalw
 	for f in clustalv.doc clustalw.doc clustalw.ms clustalw_help; do \
-		${INSTALL_DATA} ${WRKSRC}/$$f ${PREFIX}/share/doc/clustalw; \
+		${INSTALL_DATA} ${WRKSRC}/$$f \
+			${DESTDIR}${PREFIX}/share/doc/clustalw; \
 	done
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/coalesce/Makefile b/biology/coalesce/Makefile
index 85d25fbd57e..38e89e67510 100644
--- a/biology/coalesce/Makefile
+++ b/biology/coalesce/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.6 2005/06/16 06:57:40 jlam Exp $
+# $NetBSD: Makefile,v 1.7 2008/03/03 01:10:05 jlam Exp $
 #
 
 DISTNAME=	coalesce1.5b
@@ -10,6 +10,8 @@ MAINTAINER=	brook@nmsu.edu
 HOMEPAGE=	http://evolution.genetics.washington.edu/lamarc/coalesce.html
 COMMENT=	Estimates effective population size and mutation rate
 
+PKG_DESTDIR_SUPPORT=	user-destdir
+
 WRKSRC=		${WRKDIR}/coalesce1.5beta
 BUILD_TARGET=	coalesce
 
@@ -21,14 +23,14 @@ EXFILES=	bestree infile intree outfile parmfile seedfile
 INSTALLATION_DIRS=	bin
 
 do-install:
-	${INSTALL_DATA_DIR} ${DOCDIR}
-	${INSTALL_DATA_DIR} ${EXDIR}
-	${INSTALL_PROGRAM} ${WRKSRC}/coalesce ${PREFIX}/bin/
-	for f in ${DOCFILES}; do 				\
-		${INSTALL_DATA} ${WRKSRC}/$$f ${DOCDIR}/$$f; 	\
+	${INSTALL_DATA_DIR} ${DESTDIR}${DOCDIR}
+	${INSTALL_DATA_DIR} ${DESTDIR}${EXDIR}
+	${INSTALL_PROGRAM} ${WRKSRC}/coalesce ${DESTDIR}${PREFIX}/bin
+	for f in ${DOCFILES}; do 					\
+		${INSTALL_DATA} ${WRKSRC}/$$f ${DESTDIR}${DOCDIR}/$$f; 	\
 	done
-	for f in ${EXFILES}; do 				\
-		${INSTALL_DATA} ${WRKSRC}/$$f ${EXDIR}/$$f; 	\
+	for f in ${EXFILES}; do 					\
+		${INSTALL_DATA} ${WRKSRC}/$$f ${DESTDIR}${EXDIR}/$$f; 	\
 	done
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/fastDNAml/Makefile b/biology/fastDNAml/Makefile
index ef7ec12fc43..4e80c773e7a 100644
--- a/biology/fastDNAml/Makefile
+++ b/biology/fastDNAml/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.8 2005/06/16 06:57:40 jlam Exp $
+# $NetBSD: Makefile,v 1.9 2008/03/03 01:10:05 jlam Exp $
 
 DISTNAME=	fastDNAml_1.2.2
 PKGNAME=	fastDNAml-1.2.2
@@ -9,12 +9,14 @@ MAINTAINER=	babafou@babafou.eu.org
 HOMEPAGE=	http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html
 COMMENT=	Program derived from Joseph Felsenstein's version 3.3 DNAML
 
+PKG_DESTDIR_SUPPORT=	user-destdir
+
 WRKSRC=		${WRKDIR}/${DISTNAME}/source
 
 INSTALLATION_DIRS=	bin
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/fastDNAml ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/fastDNAml ${DESTDIR}${PREFIX}/bin
 .for SCRIPT in ae2dnaml bootstrap categories categories_file		\
 		checkpoint_summary clean_checkpoints clean_jumbles	\
 		dnaml_progress fastDNAml_boot fastDNAml_loop		\
@@ -23,11 +25,13 @@ do-install:
 		quickadd restart scores transition treefile		\
 		treefile2prolog trees2NEXUS trees2prolog userlengths	\
 		usertree usertrees weights weights_categories
-	${INSTALL_SCRIPT} ${WRKDIR}/${DISTNAME}/scripts/${SCRIPT} ${PREFIX}/bin
+	${INSTALL_SCRIPT} ${WRKDIR}/${DISTNAME}/scripts/${SCRIPT}	\
+		${DESTDIR}${PREFIX}/bin
 .endfor
-	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/fastDNAml
+	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/fastDNAml
 .for DOC in fastDNAml_doc_1.2.txt fastDNAml_scripts.txt
-	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/docs/${DOC} ${PREFIX}/share/doc/fastDNAml
+	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/docs/${DOC}		\
+		${DESTDIR}${PREFIX}/share/doc/fastDNAml
 .endfor
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/fluctuate/Makefile b/biology/fluctuate/Makefile
index 5d3d0d9a388..4e608478835 100644
--- a/biology/fluctuate/Makefile
+++ b/biology/fluctuate/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.7 2007/11/06 20:16:58 reed Exp $
+# $NetBSD: Makefile,v 1.8 2008/03/03 01:10:05 jlam Exp $
 #
 
 DISTNAME=	fluctuate1.4.src.doc
@@ -10,6 +10,8 @@ MAINTAINER=	brook@nmsu.edu
 HOMEPAGE=	http://evolution.genetics.washington.edu/lamarc/fluctuate.html
 COMMENT=	Estimation of population growth rate
 
+PKG_DESTDIR_SUPPORT=	user-destdir
+
 WRKSRC=		${WRKDIR}/fluctuate1.4
 BUILD_TARGET=	fluctuate
 
@@ -21,14 +23,14 @@ EXFILES=	bestree infile outfile
 INSTALLATION_DIRS=	bin
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/fluctuate ${PREFIX}/bin/
-	${INSTALL_DATA_DIR} ${DOCDIR}
-	${INSTALL_DATA_DIR} ${EXDIR}
-	for f in ${DOCFILES}; do 				\
-		${INSTALL_DATA} ${WRKSRC}/$$f ${DOCDIR}/$$f; 	\
+	${INSTALL_PROGRAM} ${WRKSRC}/fluctuate ${DESTDIR}${PREFIX}/bin
+	${INSTALL_DATA_DIR} ${DESTDIR}${DOCDIR}
+	${INSTALL_DATA_DIR} ${DESTDIR}${EXDIR}
+	for f in ${DOCFILES}; do 					\
+		${INSTALL_DATA} ${WRKSRC}/$$f ${DESTDIR}${DOCDIR}/$$f; 	\
 	done
-	for f in ${EXFILES}; do 				\
-		${INSTALL_DATA} ${WRKSRC}/$$f ${EXDIR}/$$f; 	\
+	for f in ${EXFILES}; do 					\
+		${INSTALL_DATA} ${WRKSRC}/$$f ${DESTDIR}${EXDIR}/$$f; 	\
 	done
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/genesplicer/Makefile b/biology/genesplicer/Makefile
index dc757be4438..85eac030346 100644
--- a/biology/genesplicer/Makefile
+++ b/biology/genesplicer/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.9 2006/09/09 02:41:55 obache Exp $
+# $NetBSD: Makefile,v 1.10 2008/03/03 01:10:05 jlam Exp $
 #
 
 DISTNAME=		GeneSplicer
@@ -10,6 +10,8 @@ MAINTAINER=		hdp@cs.nmsu.edu
 HOMEPAGE=		ftp://ftp.tigr.org/pub/software/GeneSplicer/
 COMMENT=		Computational Method for Splice Site Prediction
 
+PKG_DESTDIR_SUPPORT=	user-destdir
+
 USE_LANGUAGES=		c c++
 
 EXDIR=			${PREFIX}/share/examples/genesplicer
@@ -21,11 +23,11 @@ BUILD_DIRS=		sources
 INSTALLATION_DIRS=	bin
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/sources/genesplicer ${PREFIX}/bin
-	${INSTALL_DATA_DIR} ${EXDIR}
+	${INSTALL_PROGRAM} ${WRKSRC}/sources/genesplicer ${DESTDIR}${PREFIX}/bin
+	${INSTALL_DATA_DIR} ${DESTDIR}${EXDIR}
 .for DOC in readme fasta.example fasta.results
-	${INSTALL_DATA} ${WRKSRC}/sources/${DOC} ${EXDIR}
+	${INSTALL_DATA} ${WRKSRC}/sources/${DOC} ${DESTDIR}${EXDIR}
 .endfor
-	cd ${WRKSRC} && ${PAX} -rw ${EXAMPLES} ${EXDIR}/
+	cd ${WRKSRC} && ${PAX} -rw ${EXAMPLES} ${DESTDIR}${EXDIR}
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/glimmer/Makefile b/biology/glimmer/Makefile
index 8009c97f48d..4a532ff2c11 100644
--- a/biology/glimmer/Makefile
+++ b/biology/glimmer/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.9 2007/02/22 19:26:09 wiz Exp $
+# $NetBSD: Makefile,v 1.10 2008/03/03 01:10:06 jlam Exp $
 #
 
 DISTNAME=		glimmer213
@@ -10,6 +10,8 @@ MAINTAINER=		hdp@cs.nmsu.edu
 HOMEPAGE=		ftp://ftp.tigr.org/pub/software/Glimmer/
 COMMENT=		System for finding genes in microbial DNA
 
+PKG_DESTDIR_SUPPORT=	user-destdir
+
 USE_LANGUAGES=		c c++
 
 WRKSRC=			${WRKDIR}/glimmer2.13
@@ -18,16 +20,16 @@ INSTALLATION_DIRS=	bin
 do-install:
 .for PROGRAM in adjust anomaly build-icm check codon-usage compare-lists \
 	generate get-len get-putative glimmer2 long-orfs
-	${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${DESTDIR}${PREFIX}/bin
 .endfor
 	# ``extract'' is also in the csound package, so rename to avoid conflict
-	${INSTALL_PROGRAM} ${WRKSRC}/extract ${PREFIX}/bin/glextract
-	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/glimmer
+	${INSTALL_PROGRAM} ${WRKSRC}/extract ${DESTDIR}${PREFIX}/bin/glextract
+	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/glimmer
 	${CP} ${WRKSRC}/README ${WRKSRC}/run-glimmer2.readme
 .for DOC in run-glimmer2.readme build-icm.readme extract.readme glimmer2.readme long-orfs.readme
-	${INSTALL_DATA} ${WRKSRC}/${DOC} ${PREFIX}/share/doc/glimmer
+	${INSTALL_DATA} ${WRKSRC}/${DOC} ${DESTDIR}${PREFIX}/share/doc/glimmer
 .endfor
-	${INSTALL_DATA_DIR} ${PREFIX}/share/glimmer
-	${INSTALL_SCRIPT} ${WRKSRC}/run-glimmer2 ${PREFIX}/share/glimmer
+	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/glimmer
+	${INSTALL_SCRIPT} ${WRKSRC}/run-glimmer2 ${DESTDIR}${PREFIX}/share/glimmer
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/lucy/Makefile b/biology/lucy/Makefile
index c4fdbd79050..05619da372f 100644
--- a/biology/lucy/Makefile
+++ b/biology/lucy/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.3 2007/01/07 09:13:48 rillig Exp $
+# $NetBSD: Makefile,v 1.4 2008/03/03 01:10:06 jlam Exp $
 #
 
 DISTNAME=		lucy-1.18p
@@ -10,17 +10,19 @@ HOMEPAGE=		http://www.tigr.org/software/
 COMMENT=		Sequence Cleanup Program
 
 PKG_INSTALLATION_TYPES=	overwrite pkgviews
+PKG_DESTDIR_SUPPORT=	user-destdir
 
 INSTALLATION_DIRS=	bin ${PKGMANDIR}/man1
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/lucy ${PREFIX}/bin
-	${INSTALL_DATA} ${WRKSRC}/lucy.1 ${PREFIX}/${PKGMANDIR}/man1
-	${INSTALL_DATA_DIR} ${PREFIX}/share/examples/lucy
+	${INSTALL_PROGRAM} ${WRKSRC}/lucy ${DESTDIR}${PREFIX}/bin
+	${INSTALL_DATA} ${WRKSRC}/lucy.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
+	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/examples/lucy
 .for EXAMPLE in PUC19 PUC19splice PUC19splice.for PUC19splice.rev \
 	atie.seq atie.qul atie.2nd pSPORT1splice pSPORT1vector ARMTM40TR.seq \
 	ARMTM40TR.qul lucy.ps lucy.debug
-	${INSTALL_DATA} ${WRKSRC}/${EXAMPLE} ${PREFIX}/share/examples/lucy
+	${INSTALL_DATA} ${WRKSRC}/${EXAMPLE} \
+		${DESTDIR}${PREFIX}/share/examples/lucy
 .endfor
 
 .include "../../mk/pthread.buildlink3.mk"
diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile
index 97281c2c9c3..cd54bbe48dd 100644
--- a/biology/mummer/Makefile
+++ b/biology/mummer/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.15 2007/01/18 19:13:10 rillig Exp $
+# $NetBSD: Makefile,v 1.16 2008/03/03 01:10:06 jlam Exp $
 #
 
 DISTNAME=		MUMmer3.19
@@ -10,6 +10,8 @@ MAINTAINER=		hdp@cs.nmsu.edu
 HOMEPAGE=		http://mummer.sourceforge.net/
 COMMENT=		System for aligning whole genome sequences
 
+PKG_DESTDIR_SUPPORT=	user-destdir
+
 WRKSRC=			${WRKDIR}/${DISTNAME}
 USE_TOOLS+=		csh:run gmake perl:run
 USE_LANGUAGES=		c c++
@@ -22,15 +24,16 @@ INSTALLATION_DIRS=	bin share/doc/mummer share/mummer
 do-install:
 .for p in annotate combineMUMs delta-filter gaps mgaps mummer \
 	repeat-match show-aligns show-coords show-snps show-tiling
-	${INSTALL_PROGRAM} ${WRKSRC}/${p} ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/${p} ${DESTDIR}${PREFIX}/bin
 .endfor
 .for p in postnuc postpro prenuc prepro
-	${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/${p} ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/${p} ${DESTDIR}${PREFIX}/bin
 .endfor
 .for f in run-mummer1 run-mummer3 nucmer promer exact-tandems 	  \
 	mapview mummerplot nucmer2xfig
-	${INSTALL_SCRIPT} ${WRKSRC}/${f} ${PREFIX}/share/mummer
+	${INSTALL_SCRIPT} ${WRKSRC}/${f} ${DESTDIR}${PREFIX}/share/mummer
 .endfor
-	cd ${WRKSRC}/docs && pax -wr -s ',^Makefile$$,,' * ${PREFIX}/share/doc/mummer
+	cd ${WRKSRC}/docs && pax -wr -s ',^Makefile$$,,' * \
+		${DESTDIR}${PREFIX}/share/doc/mummer
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/pdbalign/Makefile b/biology/pdbalign/Makefile
index e0cbce296a2..a8cfeeafa55 100644
--- a/biology/pdbalign/Makefile
+++ b/biology/pdbalign/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.4 2007/02/22 19:26:09 wiz Exp $
+# $NetBSD: Makefile,v 1.5 2008/03/03 01:10:06 jlam Exp $
 #
 
 DISTNAME=		pdbalign
@@ -10,12 +10,14 @@ MAINTAINER=		hdp@cs.nmsu.edu
 HOMEPAGE=		#empty
 COMMENT=		Prediction of Protein Secondary Structure and Active Sites
 
+PKG_DESTDIR_SUPPORT=	user-destdir
+
 WRKSRC=			${WRKDIR}
 INSTALLATION_DIRS=	bin
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/pdbalign ${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/distalign ${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/pdbdist ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/pdbalign ${DESTDIR}${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/distalign ${DESTDIR}${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/pdbdist ${DESTDIR}${PREFIX}/bin
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile
index ae7d8ca806a..585777b4de9 100644
--- a/biology/phylip/Makefile
+++ b/biology/phylip/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.16 2007/01/26 22:06:38 joerg Exp $
+# $NetBSD: Makefile,v 1.17 2008/03/03 01:10:06 jlam Exp $
 
 DISTNAME=	phylip-3.61
 PKGREVISION=	2
@@ -14,6 +14,8 @@ RESTRICTED=		No commercial distribution without a royalty agreement with the aut
 NO_SRC_ON_CDROM=	${RESTRICTED}
 NO_BIN_ON_CDROM=	${RESTRICTED}
 
+PKG_DESTDIR_SUPPORT=	user-destdir
+
 WRKSRC=		${WRKDIR}/${DISTNAME}/src
 
 INSTALLATION_DIRS=	bin
@@ -25,14 +27,14 @@ do-install:
 		mix move neighbor pars penny proml promlk protdist	\
 		protpars restdist restml retree seqboot treedist	\
 		drawgram drawtree
-	${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${DESTDIR}${PREFIX}/bin
 .endfor
-	${INSTALL_DATA_DIR} ${PREFIX}/share/fonts/phylip
+	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/fonts/phylip
 .for FONT in font1 font2 font3 font4 font5 font6
-	${INSTALL_DATA} ${WRKSRC}/${FONT} ${PREFIX}/share/fonts/phylip
+	${INSTALL_DATA} ${WRKSRC}/${FONT} ${DESTDIR}${PREFIX}/share/fonts/phylip
 .endfor
 	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/phylip
-.for HTML in clique.html consense.html contchar.html contml.html		\
+.for HTML in clique.html consense.html contchar.html contml.html	\
 		contrast.html discrete.html distance.html dnacomp.html	\
 		dnadist.html dnainvar.html dnaml.html dnamlk.html	\
 		dnamove.html dnapars.html dnapenny.html dollop.html	\
@@ -43,7 +45,8 @@ do-install:
 		promlk.html protdist.html protpars.html restdist.html	\
 		restml.html retree.html seqboot.html sequence.html	\
 		treedist.html
-	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/doc/${HTML} ${PREFIX}/share/doc/html/phylip
+	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/doc/${HTML}		\
+		${DESTDIR}${PREFIX}/share/doc/html/phylip
 .endfor
 
 MAKE_ENV+=	X11_LDFLAGS=${X11_LDFLAGS:Q}
diff --git a/biology/profit/Makefile b/biology/profit/Makefile
index bd71de5f1c4..de83c8fa31c 100644
--- a/biology/profit/Makefile
+++ b/biology/profit/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.9 2005/11/03 19:45:20 rillig Exp $
+# $NetBSD: Makefile,v 1.10 2008/03/03 01:10:06 jlam Exp $
 #
 
 DISTNAME=		ProFitV2.2
@@ -10,18 +10,21 @@ MAINTAINER=		hdp@cs.nmsu.edu
 HOMEPAGE=		http://acrmwww.biochem.ucl.ac.uk/programs/profit/index.html
 COMMENT=		Performs least squares fits of two protein structures
 
+PKG_DESTDIR_SUPPORT=	user-destdir
+
 BUILD_TARGET=		profit
 BUILD_DIRS=		src
 INSTALLATION_DIRS=	bin
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/src/profit ${PREFIX}/bin
-	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/profit
+	${INSTALL_PROGRAM} ${WRKSRC}/src/profit ${DESTDIR}${PREFIX}/bin
+	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/profit
 .for sufx in dvi ps tex
-	${INSTALL_DATA} ${WRKSRC}/doc/ProFit.${sufx} ${PREFIX}/share/doc/profit
+	${INSTALL_DATA} ${WRKSRC}/doc/ProFit.${sufx}			\
+		${DESTDIR}${PREFIX}/share/doc/profit
 .endfor
-	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/profit
+	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/html/profit
 	cd ${WRKSRC}/doc/ProFit/ && 					\
-		${PAX} -rw . ${PREFIX}/share/doc/html/profit/
+		${PAX} -rw . ${DESTDIR}${PREFIX}/share/doc/html/profit/
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/sewer/Makefile b/biology/sewer/Makefile
index 02f404f716b..a9169a1100f 100644
--- a/biology/sewer/Makefile
+++ b/biology/sewer/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.5 2006/02/05 23:08:20 joerg Exp $
+# $NetBSD: Makefile,v 1.6 2008/03/03 01:10:06 jlam Exp $
 
 DISTNAME=		sewer
 PKGNAME=		sewer-2.6
@@ -12,6 +12,7 @@ HOMEPAGE=		http://iubio.bio.indiana.edu/webapps/SeWeR/
 COMMENT=		SEquence Analysis using WEb Resources
 
 PKG_INSTALLATION_TYPES=	overwrite pkgviews
+PKG_DESTDIR_SUPPORT=	user-destdir
 
 NO_CONFIGURE=		YES
 NO_BUILD=		YES
@@ -24,8 +25,10 @@ pre-install:
 .endfor
 
 do-install:
-	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/sewer
-	cd ${WRKDIR} && ${PAX} -rw [a-z]* ${PREFIX}/share/doc/html/sewer/
-	cd ${PREFIX}/share/doc/html/sewer && ${LN} -s sewer.htm index.html
+	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/html/sewer
+	cd ${WRKDIR} && ${PAX} -rw [a-z]* \
+		${DESTDIR}${PREFIX}/share/doc/html/sewer/
+	cd ${DESTDIR}${PREFIX}/share/doc/html/sewer && \
+		${LN} -s sewer.htm index.html
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/stride/Makefile b/biology/stride/Makefile
index 03e990d1d22..23c6bcafaae 100644
--- a/biology/stride/Makefile
+++ b/biology/stride/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.6 2005/06/16 06:57:41 jlam Exp $
+# $NetBSD: Makefile,v 1.7 2008/03/03 01:10:06 jlam Exp $
 #
 
 DISTNAME=		stride
@@ -10,10 +10,12 @@ MAINTAINER=		hdp@cs.nmsu.edu
 HOMEPAGE=		http://wolf.bi.umist.ac.uk/unix/stride.html
 COMMENT=		Protein secondary structure assignment from atomic coordinates
 
+PKG_DESTDIR_SUPPORT=	user-destdir
+
 WRKSRC=			${WRKDIR}
 INSTALLATION_DIRS=	bin
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKDIR}/stride ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKDIR}/stride ${DESTDIR}${PREFIX}/bin
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/xylem/Makefile b/biology/xylem/Makefile
index 4f07a820766..58a674e3a03 100644
--- a/biology/xylem/Makefile
+++ b/biology/xylem/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.7 2007/02/22 19:26:09 wiz Exp $
+# $NetBSD: Makefile,v 1.8 2008/03/03 01:10:06 jlam Exp $
 #
 
 DISTNAME=		xylem.1.8.7
@@ -11,6 +11,8 @@ MAINTAINER=		hdp@cs.nmsu.edu
 HOMEPAGE=		http://home.cc.umanitoba.ca/~psgendb/XYLEM.html
 COMMENT=		Tools for manipulation of genetic databases
 
+PKG_DESTDIR_SUPPORT=	user-destdir
+
 WRKSRC=			${WRKDIR}/xylem
 BUILD_DIRS=		src.c # yes, it's a directory
 INSTALLATION_DIRS=	bin
@@ -27,12 +29,14 @@ post-build:
 do-install:
 .for PROGRAM in dbstat getloc getob xyl-identify prot2nuc reform ribosome \
 	splitdb xyl-shuffle flat2phyl phyl2flat
-	${INSTALL_PROGRAM} ${WRKSRC}/src.c/${PROGRAM} ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/src.c/${PROGRAM} ${DESTDIR}${PREFIX}/bin
 .endfor
-	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/xylem
-	${INSTALL_DATA} ${WRKSRC}/doc/* ${PREFIX}/share/doc/xylem/
-	${INSTALL_DATA_DIR} ${PREFIX}/share/examples/xylem
-	${INSTALL_DATA} ${WRKSRC}/test/sample.* ${PREFIX}/share/examples/xylem
-	${INSTALL_SCRIPT} ${WRKSRC}/test/testxylem.csh ${PREFIX}/share/examples/xylem
+	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/xylem
+	${INSTALL_DATA} ${WRKSRC}/doc/* ${DESTDIR}${PREFIX}/share/doc/xylem/
+	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/examples/xylem
+	${INSTALL_DATA} ${WRKSRC}/test/sample.* \
+		${DESTDIR}${PREFIX}/share/examples/xylem
+	${INSTALL_SCRIPT} ${WRKSRC}/test/testxylem.csh \
+		${DESTDIR}${PREFIX}/share/examples/xylem
 
 .include "../../mk/bsd.pkg.mk"