Second round of explicit pax dependencies. As reminded by tnn@,

many packages used to use ${PAX}. Use the common way of directly calling
pax, it is created as tool after all.

5 files changed, 19 insertions, 12 deletions

diff --git a/biology/bioperl/Makefile b/biology/bioperl/Makefile
index 9cf00438ec7..421d2231b54 100644
--- a/biology/bioperl/Makefile
+++ b/biology/bioperl/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.15 2006/06/05 23:34:42 minskim Exp $
+# $NetBSD: Makefile,v 1.16 2008/05/26 02:13:16 joerg Exp $
 #
 
 DISTNAME=		bioperl-0.7.0
@@ -10,6 +10,8 @@ MAINTAINER=		pkgsrc-users@NetBSD.org
 HOMEPAGE=		http://bioperl.org/
 COMMENT=		Perl tools for computational molecular biology
 
+USE_TOOLS+=	pax
+
 REPLACE_PERL+=		Bio/LiveSeq/Chain.pm
 REPLACE_PERL+=		Bio/SeqIO/game/featureHandler.pm
 REPLACE_PERL+=		Bio/Tools/Blast/Run/postclient.pl
@@ -24,7 +26,7 @@ PERL5_PACKLIST=		auto/Bio/.packlist
 
 post-install:
 	${INSTALL_DATA_DIR} ${PREFIX}/share/examples/bioperl
-	cd ${WRKSRC}/examples && ${PAX} -rw . ${PREFIX}/share/examples/bioperl
+	cd ${WRKSRC}/examples && pax -rw . ${PREFIX}/share/examples/bioperl
 
 .include "../../lang/perl5/module.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/genesplicer/Makefile b/biology/genesplicer/Makefile
index 85eac030346..c59e199d035 100644
--- a/biology/genesplicer/Makefile
+++ b/biology/genesplicer/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.10 2008/03/03 01:10:05 jlam Exp $
+# $NetBSD: Makefile,v 1.11 2008/05/26 02:13:16 joerg Exp $
 #
 
 DISTNAME=		GeneSplicer
@@ -13,6 +13,7 @@ COMMENT=		Computational Method for Splice Site Prediction
 PKG_DESTDIR_SUPPORT=	user-destdir
 
 USE_LANGUAGES=		c c++
+USE_TOOLS+=		pax
 
 EXDIR=			${PREFIX}/share/examples/genesplicer
 EXAMPLES=		arabidopsis drosophila malaria pyoelii human rice \
@@ -28,6 +29,6 @@ do-install:
 .for DOC in readme fasta.example fasta.results
 	${INSTALL_DATA} ${WRKSRC}/sources/${DOC} ${DESTDIR}${EXDIR}
 .endfor
-	cd ${WRKSRC} && ${PAX} -rw ${EXAMPLES} ${DESTDIR}${EXDIR}
+	cd ${WRKSRC} && pax -rw ${EXAMPLES} ${DESTDIR}${EXDIR}
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/mopac/Makefile b/biology/mopac/Makefile
index d937361fc90..708d8e87d3a 100644
--- a/biology/mopac/Makefile
+++ b/biology/mopac/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.1.1.1 2008/03/09 17:52:57 tnn Exp $
+# $NetBSD: Makefile,v 1.2 2008/05/26 02:13:16 joerg Exp $
 #
 
 DISTNAME=		mopac7
@@ -20,7 +20,7 @@ PKG_DESTDIR_SUPPORT=	user-destdir
 
 WRKSRC=			${WRKDIR}/mopac7
 BUILD_TARGET=		MOPAC7
-USE_TOOLS+=		gmake
+USE_TOOLS+=		gmake pax
 USE_LANGUAGES=		fortran
 PKG_FC=			f2c-f77
 
@@ -34,9 +34,9 @@ pre-build:
 do-install:
 	${INSTALL_SCRIPT} ${WRKSRC}/mopac ${DESTDIR}${PREFIX}/bin
 	${INSTALL_PROGRAM} ${WRKSRC}/MOPAC7 ${DESTDIR}${PREFIX}/bin
-	cd ${WRKSRC} && ${PAX} -wr test_* \
+	cd ${WRKSRC} && pax -wr test_* \
 	  ${DESTDIR}${PREFIX}/share/mopac7/sample
-	cd ${WRKDIR} && ${PAX} -wr mopac7-man ${DESTDIR}${PREFIX}/share/mopac7
+	cd ${WRKDIR} && pax -wr mopac7-man ${DESTDIR}${PREFIX}/share/mopac7
 
 # "g77" can not be used for external function
 
diff --git a/biology/profit/Makefile b/biology/profit/Makefile
index de83c8fa31c..8d47c3df322 100644
--- a/biology/profit/Makefile
+++ b/biology/profit/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.10 2008/03/03 01:10:06 jlam Exp $
+# $NetBSD: Makefile,v 1.11 2008/05/26 02:13:16 joerg Exp $
 #
 
 DISTNAME=		ProFitV2.2
@@ -12,6 +12,8 @@ COMMENT=		Performs least squares fits of two protein structures
 
 PKG_DESTDIR_SUPPORT=	user-destdir
 
+USE_TOOLS+=	pax
+
 BUILD_TARGET=		profit
 BUILD_DIRS=		src
 INSTALLATION_DIRS=	bin
@@ -25,6 +27,6 @@ do-install:
 .endfor
 	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/html/profit
 	cd ${WRKSRC}/doc/ProFit/ && 					\
-		${PAX} -rw . ${DESTDIR}${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 a9169a1100f..bbae6bd69de 100644
--- a/biology/sewer/Makefile
+++ b/biology/sewer/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.6 2008/03/03 01:10:06 jlam Exp $
+# $NetBSD: Makefile,v 1.7 2008/05/26 02:13:16 joerg Exp $
 
 DISTNAME=		sewer
 PKGNAME=		sewer-2.6
@@ -14,6 +14,8 @@ COMMENT=		SEquence Analysis using WEb Resources
 PKG_INSTALLATION_TYPES=	overwrite pkgviews
 PKG_DESTDIR_SUPPORT=	user-destdir
 
+USE_TOOLS+=	pax
+
 NO_CONFIGURE=		YES
 NO_BUILD=		YES
 
@@ -26,7 +28,7 @@ pre-install:
 
 do-install:
 	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/html/sewer
-	cd ${WRKDIR} && ${PAX} -rw [a-z]* \
+	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