Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

38 files changed, 148 insertions, 148 deletions

diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile
index ff969014a35e..e0b804b87190 100644
--- a/biology/bcftools/Makefile
+++ b/biology/bcftools/Makefile
@@ -11,9 +11,9 @@ COMMENT=	Tools for manipulating next-generation sequencing data
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-BUILD_DEPENDS=	htslib>=1.3:${PORTSDIR}/biology/htslib
-LIB_DEPENDS=	libhts.so:${PORTSDIR}/biology/htslib
-TEST_DEPENDS=	bash:${PORTSDIR}/shells/bash
+BUILD_DEPENDS=	htslib>=1.3:biology/htslib
+LIB_DEPENDS=	libhts.so:biology/htslib
+TEST_DEPENDS=	bash:shells/bash
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	samtools
@@ -27,7 +27,7 @@ OPTIONS_DEFINE=	GPL
 GPL_DESC=	Enable modules that rely on GPL code
 OPTIONS_DEFAULT=	GPL
 
-GPL_LIB_DEPENDS=	libgsl.so:${PORTSDIR}/math/gsl
+GPL_LIB_DEPENDS=	libgsl.so:math/gsl
 
 .include <bsd.port.options.mk>
 
diff --git a/biology/blat/Makefile b/biology/blat/Makefile
index db878287c9e9..7d8cb309bdb9 100644
--- a/biology/blat/Makefile
+++ b/biology/blat/Makefile
@@ -11,7 +11,7 @@ DISTNAME=	${PORTNAME}Src${PORTVERSION}
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Fast tool for local sequence similarity searches
 
-LIB_DEPENDS=	libpng.so:${PORTSDIR}/graphics/png
+LIB_DEPENDS=	libpng.so:graphics/png
 
 OPTIONS_DEFINE=	DOCS
 
diff --git a/biology/consed/Makefile b/biology/consed/Makefile
index c45aee4933d2..19d4b93e0c86 100644
--- a/biology/consed/Makefile
+++ b/biology/consed/Makefile
@@ -11,8 +11,8 @@ DISTNAME=	${PORTNAME}_linux
 MAINTAINER=	mzaki@m.u-tokyo.ac.jp
 COMMENT=	Graphical tool for editing Phrap assemblies
 
-RUN_DEPENDS=	phred:${PORTSDIR}/biology/phred \
-		phrap:${PORTSDIR}/biology/phrap
+RUN_DEPENDS=	phred:biology/phred \
+		phrap:biology/phrap
 
 CONFLICTS_INSTALL=	phd2fasta-[0-9]*
 
diff --git a/biology/crux/Makefile b/biology/crux/Makefile
index c8eaac6ecedb..6f6ee97b8db1 100644
--- a/biology/crux/Makefile
+++ b/biology/crux/Makefile
@@ -28,7 +28,7 @@ MAKE_JOBS_UNSAFE=	yes
 OPTIONS_DEFINE=		SYS_LINALG
 
 SYS_LINALG_DESC=	Enable system ATLAS/LAPACK
-SYS_LINALG_LIB_DEPENDS=	libatlas.so:${PORTSDIR}/math/atlas
+SYS_LINALG_LIB_DEPENDS=	libatlas.so:math/atlas
 SYS_LINALG_CONFIGURE_ENABLE=	sys-linalg
 
 post-patch:
diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index 5eae33585420..447981d0fb28 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -14,10 +14,10 @@ COMMENT=	Collection of open source tools for genetic sequence analysis
 
 LICENSE=	GPLv2
 
-BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw \
-		primer3:${PORTSDIR}/biology/primer3
-LIB_DEPENDS=	libgd.so:${PORTSDIR}/graphics/gd \
-		libpng.so:${PORTSDIR}/graphics/png
+BUILD_DEPENDS=	clustalw:biology/clustalw \
+		primer3:biology/primer3
+LIB_DEPENDS=	libgd.so:graphics/gd \
+		libpng.so:graphics/png
 
 CONFLICTS=	qmail-ldap-[0-9]* digest-[0-9]*
 
@@ -41,8 +41,8 @@ OPTIONS_DEFAULT=	X11
 DOCS_CONFIGURE_ON=	--with-docroot=${DOCSDIR}
 X11_USE=	XORG=x11
 X11_USES=	motif
-X11_LIB_DEPENDS=	libgd.so:${PORTSDIR}/graphics/gd \
-		libpng.so:${PORTSDIR}/graphics/png
+X11_LIB_DEPENDS=	libgd.so:graphics/gd \
+		libpng.so:graphics/png
 X11_CONFIGURE_OFF=	--without-x
 
 CONFIG_FILE=	${WRKSRC}/emboss/emboss.default.template
diff --git a/biology/fastx-toolkit/Makefile b/biology/fastx-toolkit/Makefile
index ed8f59c689c1..e8f9f97e8aa5 100644
--- a/biology/fastx-toolkit/Makefile
+++ b/biology/fastx-toolkit/Makefile
@@ -11,7 +11,7 @@ COMMENT=	CLI tools for Short-Reads FASTA/FASTQ files preprocessing
 LICENSE=	AGPLv3+
 LICENSE_FILE=	${WRKSRC}/COPYING
 
-LIB_DEPENDS=	libgtextutils.so:${PORTSDIR}/biology/libgtextutils
+LIB_DEPENDS=	libgtextutils.so:biology/libgtextutils
 
 USES=		autoreconf libtool perl5 pkgconfig shebangfix
 USE_PERL5=	run
diff --git a/biology/gff2ps/Makefile b/biology/gff2ps/Makefile
index 411d9f05f31e..24bd35c10b9f 100644
--- a/biology/gff2ps/Makefile
+++ b/biology/gff2ps/Makefile
@@ -14,8 +14,8 @@ COMMENT=	Converts gff-formated genomic data-sets to PostScript
 
 LICENSE=	GPLv2+
 
-RUN_DEPENDS=	gawk:${PORTSDIR}/lang/gawk \
-		bash:${PORTSDIR}/shells/bash
+RUN_DEPENDS=	gawk:lang/gawk \
+		bash:shells/bash
 
 NO_WRKSUBDIR=	yes
 NO_BUILD=	yes
diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile
index b6532c2d21b8..c7a9feec1c20 100644
--- a/biology/htslib/Makefile
+++ b/biology/htslib/Makefile
@@ -12,7 +12,7 @@ LICENSE=	BSD3CLAUSE MIT
 LICENSE_COMB=	multi
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-TEST_DEPENDS=	bash:${PORTSDIR}/shells/bash
+TEST_DEPENDS=	bash:shells/bash
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	samtools
@@ -27,7 +27,7 @@ OPTIONS_DEFINE=		CURL
 OPTIONS_DEFAULT=	CURL
 
 CURL_DESC=		Use libcurl for network file access (HTTPS and S3 support).
-CURL_LIB_DEPENDS=	libcurl.so:${PORTSDIR}/ftp/curl
+CURL_LIB_DEPENDS=	libcurl.so:ftp/curl
 CURL_CONFIGURE_ENABLE=	libcurl
 
 CPPFLAGS+=	-I${LOCALBASE}/include
diff --git a/biology/iolib/Makefile b/biology/iolib/Makefile
index 26c3ccc9caf8..0bbd5eacc991 100644
--- a/biology/iolib/Makefile
+++ b/biology/iolib/Makefile
@@ -11,7 +11,7 @@ COMMENT=	General purpose trace file (and Experiment File) reading interface
 
 LICENSE=	BSD3CLAUSE
 
-LIB_DEPENDS=	libcurl.so:${PORTSDIR}/ftp/curl
+LIB_DEPENDS=	libcurl.so:ftp/curl
 
 USES=		gmake libtool
 GNU_CONFIGURE=	yes
diff --git a/biology/jellyfish/Makefile b/biology/jellyfish/Makefile
index f427a40f6a73..92c3e8e8fb0f 100644
--- a/biology/jellyfish/Makefile
+++ b/biology/jellyfish/Makefile
@@ -12,7 +12,7 @@ COMMENT=	Fast, memory-efficient counting of k-mers in DNA
 LICENSE=	GPLv3+
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-BUILD_DEPENDS=	yaggo:${PORTSDIR}/devel/yaggo
+BUILD_DEPENDS=	yaggo:devel/yaggo
 
 GNU_CONFIGURE=	yes
 
diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile
index 5162e2cc682d..e922fcbe1790 100644
--- a/biology/libsbml/Makefile
+++ b/biology/libsbml/Makefile
@@ -25,14 +25,14 @@ LDFLAGS+=	-L${ICONV_PREFIX}/lib
 OPTIONS_DEFINE=	EXAMPLES PYTHON RUBY
 OPTIONS_SUB=	yes
 
-PYTHON_BUILD_DEPENDS=	swig2.0:${PORTSDIR}/devel/swig20
+PYTHON_BUILD_DEPENDS=	swig2.0:devel/swig20
 PYTHON_USES=		python
 PYTHON_CMAKE_ON=	-DWITH_PYTHON:BOOL=ON \
 			-DPYTHON_INCLUDE_DIR:STRING="${PYTHON_INCLUDEDIR}" \
 			-DPYTHON_LIBRARY:STRING="${PYTHONBASE}/lib/lib${PYTHON_VERSION}.so" \
 			-DPYTHON_EXECUTABLE:STRING="${PYTHON_CMD}"
 
-RUBY_BUILD_DEPENDS=	swig2.0:${PORTSDIR}/devel/swig20
+RUBY_BUILD_DEPENDS=	swig2.0:devel/swig20
 RUBY_USE=		ruby=yes
 RUBY_CMAKE_ON=		-DWITH_RUBY:BOOL=ON
 
diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile
index 338b29313c50..644194dae2bf 100644
--- a/biology/ncbi-blast+/Makefile
+++ b/biology/ncbi-blast+/Makefile
@@ -16,9 +16,9 @@ COMMENT=	NCBI implementation of Basic Local Alignment Search Tool
 LICENSE=	PD
 LICENSE_FILE=	${WRKSRC}/scripts/projects/blast/LICENSE
 
-LIB_DEPENDS=	libpcre.so:${PORTSDIR}/devel/pcre \
-		libbz2.so:${PORTSDIR}/archivers/bzip2
-RUN_DEPENDS=	p5-List-MoreUtils>=0:${PORTSDIR}/lang/p5-List-MoreUtils
+LIB_DEPENDS=	libpcre.so:devel/pcre \
+		libbz2.so:archivers/bzip2
+RUN_DEPENDS=	p5-List-MoreUtils>=0:lang/p5-List-MoreUtils
 
 WRKSRC=		${WRKDIR}/${DISTNAME}/c++
 
diff --git a/biology/p5-AcePerl/Makefile b/biology/p5-AcePerl/Makefile
index dd3038541de1..8013d766b0fe 100644
--- a/biology/p5-AcePerl/Makefile
+++ b/biology/p5-AcePerl/Makefile
@@ -14,7 +14,7 @@ COMMENT=	Perl5 interface to the ACEDB genome database system
 LICENSE=	ART10 GPLv1
 LICENSE_COMB=	dual
 
-BUILD_DEPENDS=	p5-Cache-Cache>=0:${PORTSDIR}/devel/p5-Cache-Cache
+BUILD_DEPENDS=	p5-Cache-Cache>=0:devel/p5-Cache-Cache
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 MAKE_JOBS_UNSAFE=	yes
diff --git a/biology/p5-Bio-ASN1-EntrezGene/Makefile b/biology/p5-Bio-ASN1-EntrezGene/Makefile
index f5f7fc25e8dd..8785d558e0fe 100644
--- a/biology/p5-Bio-ASN1-EntrezGene/Makefile
+++ b/biology/p5-Bio-ASN1-EntrezGene/Makefile
@@ -12,7 +12,7 @@ PKGNAMEPREFIX=	p5-
 MAINTAINER=	perl@FreeBSD.org
 COMMENT=	Regular expression-based Perl Parser for NCBI Entrez Gene
 
-BUILD_DEPENDS=	p5-bioperl>=0:${PORTSDIR}/biology/p5-bioperl
+BUILD_DEPENDS=	p5-bioperl>=0:biology/p5-bioperl
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 USES=		perl5
diff --git a/biology/p5-Bio-Das-Lite/Makefile b/biology/p5-Bio-Das-Lite/Makefile
index 445e15b6a66d..26a213a1f4c8 100644
--- a/biology/p5-Bio-Das-Lite/Makefile
+++ b/biology/p5-Bio-Das-Lite/Makefile
@@ -14,9 +14,9 @@ COMMENT=	Perl extension for the DAS (HTTP+XML) Protocol
 LICENSE=	ART10 GPLv1
 LICENSE_COMB=	dual
 
-BUILD_DEPENDS=	p5-Readonly>=1.03:${PORTSDIR}/devel/p5-Readonly \
-		p5-libwww>=0:${PORTSDIR}/www/p5-libwww \
-		p5-WWW-Curl>=4.07:${PORTSDIR}/www/p5-WWW-Curl
+BUILD_DEPENDS=	p5-Readonly>=1.03:devel/p5-Readonly \
+		p5-libwww>=0:www/p5-libwww \
+		p5-WWW-Curl>=4.07:www/p5-WWW-Curl
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 USES=		perl5
diff --git a/biology/p5-Bio-Das/Makefile b/biology/p5-Bio-Das/Makefile
index 75777ff55cae..347e0b3a14b7 100644
--- a/biology/p5-Bio-Das/Makefile
+++ b/biology/p5-Bio-Das/Makefile
@@ -11,9 +11,9 @@ PKGNAMEPREFIX=	p5-
 MAINTAINER=	perl@FreeBSD.org
 COMMENT=	Client-side library for Distributed Genome Annotation System
 
-RUN_DEPENDS=	p5-HTML-Parser>=3:${PORTSDIR}/www/p5-HTML-Parser \
-		p5-bioperl>=0:${PORTSDIR}/biology/p5-bioperl \
-		p5-libwww>=5:${PORTSDIR}/www/p5-libwww
+RUN_DEPENDS=	p5-HTML-Parser>=3:www/p5-HTML-Parser \
+		p5-bioperl>=0:biology/p5-bioperl \
+		p5-libwww>=5:www/p5-libwww
 BUILD_DEPENDS:=	${RUN_DEPENDS}
 
 USES=		perl5
diff --git a/biology/p5-Bio-GFF3/Makefile b/biology/p5-Bio-GFF3/Makefile
index 42e857150553..48d684685367 100644
--- a/biology/p5-Bio-GFF3/Makefile
+++ b/biology/p5-Bio-GFF3/Makefile
@@ -14,11 +14,11 @@ COMMENT=	Fast low-level functions for parsing and formatting GFF3
 LICENSE=	ART10 GPLv1
 LICENSE_COMB=	dual
 
-BUILD_DEPENDS=	p5-File-ReadBackwards>=0:${PORTSDIR}/devel/p5-File-ReadBackwards \
-		p5-List-MoreUtils>=0:${PORTSDIR}/lang/p5-List-MoreUtils \
-		p5-URI>=0:${PORTSDIR}/net/p5-URI
+BUILD_DEPENDS=	p5-File-ReadBackwards>=0:devel/p5-File-ReadBackwards \
+		p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \
+		p5-URI>=0:net/p5-URI
 RUN_DEPENDS:=	${BUILD_DEPENDS}
-TEST_DEPENDS=	p5-IO-String>=0:${PORTSDIR}/devel/p5-IO-String
+TEST_DEPENDS=	p5-IO-String>=0:devel/p5-IO-String
 
 USES=		perl5
 USE_PERL5=	configure
diff --git a/biology/p5-Bio-Glite/Makefile b/biology/p5-Bio-Glite/Makefile
index d8c4e60be310..ed0668d44584 100644
--- a/biology/p5-Bio-Glite/Makefile
+++ b/biology/p5-Bio-Glite/Makefile
@@ -11,7 +11,7 @@ PKGNAMEPREFIX=	p5-
 MAINTAINER=	perl@FreeBSD.org
 COMMENT=	Perl Interface to G-language
 
-BUILD_DEPENDS=	p5-libwww>=5:${PORTSDIR}/www/p5-libwww
+BUILD_DEPENDS=	p5-libwww>=5:www/p5-libwww
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 USES=		perl5
diff --git a/biology/p5-Bio-Graphics/Makefile b/biology/p5-Bio-Graphics/Makefile
index e219ae594564..a6123ebb9237 100644
--- a/biology/p5-Bio-Graphics/Makefile
+++ b/biology/p5-Bio-Graphics/Makefile
@@ -13,11 +13,11 @@ COMMENT=	Generate GD Images of Bio::Seq Objects
 LICENSE=	ART10 GPLv1
 LICENSE_COMB=	dual
 
-BUILD_DEPENDS=	p5-Bio-SCF>=1.01:${PORTSDIR}/biology/p5-Bio-SCF \
-		p5-GD>=2.30:${PORTSDIR}/graphics/p5-GD \
-		p5-GD-SVG>=0.32:${PORTSDIR}/graphics/p5-GD-SVG \
-		p5-Statistics-Descriptive>=2.6:${PORTSDIR}/math/p5-Statistics-Descriptive \
-		p5-bioperl>=1.6.0:${PORTSDIR}/biology/p5-bioperl
+BUILD_DEPENDS=	p5-Bio-SCF>=1.01:biology/p5-Bio-SCF \
+		p5-GD>=2.30:graphics/p5-GD \
+		p5-GD-SVG>=0.32:graphics/p5-GD-SVG \
+		p5-Statistics-Descriptive>=2.6:math/p5-Statistics-Descriptive \
+		p5-bioperl>=1.6.0:biology/p5-bioperl
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 USES=		perl5
diff --git a/biology/p5-Bio-MAGETAB/Makefile b/biology/p5-Bio-MAGETAB/Makefile
index 6fc139d50a68..ce4faf061c89 100644
--- a/biology/p5-Bio-MAGETAB/Makefile
+++ b/biology/p5-Bio-MAGETAB/Makefile
@@ -13,19 +13,19 @@ COMMENT=	Data model and utility API for the MAGE-TAB format
 
 LICENSE=	GPLv2
 
-BUILD_DEPENDS=	p5-Date-Manip>=5.44:${PORTSDIR}/devel/p5-Date-Manip \
-		p5-DateTime>=0.43.02:${PORTSDIR}/devel/p5-DateTime \
-		p5-DateTime-Format-DateManip>=0.04:${PORTSDIR}/devel/p5-DateTime-Format-DateManip \
-		p5-Email-Valid>=0.179:${PORTSDIR}/mail/p5-Email-Valid \
-		p5-Moose>=0.43:${PORTSDIR}/devel/p5-Moose \
-		p5-MooseX-FollowPBP>=0.04:${PORTSDIR}/devel/p5-MooseX-FollowPBP \
-		p5-MooseX-Types>=0.10:${PORTSDIR}/devel/p5-MooseX-Types \
-		p5-Params-Coerce>=0.14:${PORTSDIR}/devel/p5-Params-Coerce \
-		p5-Parse-RecDescent>=1.965.001:${PORTSDIR}/devel/p5-Parse-RecDescent \
-		p5-Text-CSV_XS>=0.32:${PORTSDIR}/textproc/p5-Text-CSV_XS \
-		p5-URI>=1.35:${PORTSDIR}/net/p5-URI
+BUILD_DEPENDS=	p5-Date-Manip>=5.44:devel/p5-Date-Manip \
+		p5-DateTime>=0.43.02:devel/p5-DateTime \
+		p5-DateTime-Format-DateManip>=0.04:devel/p5-DateTime-Format-DateManip \
+		p5-Email-Valid>=0.179:mail/p5-Email-Valid \
+		p5-Moose>=0.43:devel/p5-Moose \
+		p5-MooseX-FollowPBP>=0.04:devel/p5-MooseX-FollowPBP \
+		p5-MooseX-Types>=0.10:devel/p5-MooseX-Types \
+		p5-Params-Coerce>=0.14:devel/p5-Params-Coerce \
+		p5-Parse-RecDescent>=1.965.001:devel/p5-Parse-RecDescent \
+		p5-Text-CSV_XS>=0.32:textproc/p5-Text-CSV_XS \
+		p5-URI>=1.35:net/p5-URI
 RUN_DEPENDS:=	${BUILD_DEPENDS}
-TEST_DEPENDS=	p5-Test-Exception>=0.26:${PORTSDIR}/devel/p5-Test-Exception
+TEST_DEPENDS=	p5-Test-Exception>=0.26:devel/p5-Test-Exception
 
 USES=		perl5
 USE_PERL5=	configure
diff --git a/biology/p5-Bio-NEXUS/Makefile b/biology/p5-Bio-NEXUS/Makefile
index b4d20deaf394..bba1732dbd31 100644
--- a/biology/p5-Bio-NEXUS/Makefile
+++ b/biology/p5-Bio-NEXUS/Makefile
@@ -11,12 +11,12 @@ PKGNAMEPREFIX=	p5-
 MAINTAINER=	perl@FreeBSD.org
 COMMENT=	Object-oriented Perl API for the NEXUS file format
 
-BUILD_DEPENDS=	p5-Clone-PP>=1.02:${PORTSDIR}/devel/p5-Clone-PP
+BUILD_DEPENDS=	p5-Clone-PP>=1.02:devel/p5-Clone-PP
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
-TEST_DEPENDS=	p5-Test-Deep>=0.106:${PORTSDIR}/devel/p5-Test-Deep \
-		p5-Test-Pod>=0:${PORTSDIR}/devel/p5-Test-Pod \
-		p5-Test-Pod-Coverage>=0:${PORTSDIR}/devel/p5-Test-Pod-Coverage
+TEST_DEPENDS=	p5-Test-Deep>=0.106:devel/p5-Test-Deep \
+		p5-Test-Pod>=0:devel/p5-Test-Pod \
+		p5-Test-Pod-Coverage>=0:devel/p5-Test-Pod-Coverage
 
 USES=		perl5
 USE_PERL5=	configure
diff --git a/biology/p5-Bio-Phylo/Makefile b/biology/p5-Bio-Phylo/Makefile
index 5ce60754c885..b697fa1d97bc 100644
--- a/biology/p5-Bio-Phylo/Makefile
+++ b/biology/p5-Bio-Phylo/Makefile
@@ -13,19 +13,19 @@ COMMENT=	Phylogenetic analysis using Perl
 LICENSE=	ART10 GPLv1
 LICENSE_COMB=	dual
 
-BUILD_DEPENDS=	p5-GD>=0:${PORTSDIR}/graphics/p5-GD \
-		p5-Math-CDF>=0:${PORTSDIR}/math/p5-Math-CDF \
-		p5-Math-Random>=0:${PORTSDIR}/math/p5-Math-Random \
-		p5-PDF-API2>=0:${PORTSDIR}/textproc/p5-PDF-API2 \
-		p5-SVG>=0:${PORTSDIR}/textproc/p5-SVG \
-		p5-SWF-Builder>=0:${PORTSDIR}/graphics/p5-SWF-Builder \
-		p5-XML-LibXML>=0:${PORTSDIR}/textproc/p5-XML-LibXML \
-		p5-XML-Twig>=0:${PORTSDIR}/textproc/p5-XML-Twig \
-		p5-XML-XML2JSON>=0:${PORTSDIR}/textproc/p5-XML-XML2JSON \
-		p5-bioperl>=0:${PORTSDIR}/biology/p5-bioperl \
-		p5-libxml>=0:${PORTSDIR}/textproc/p5-libxml
+BUILD_DEPENDS=	p5-GD>=0:graphics/p5-GD \
+		p5-Math-CDF>=0:math/p5-Math-CDF \
+		p5-Math-Random>=0:math/p5-Math-Random \
+		p5-PDF-API2>=0:textproc/p5-PDF-API2 \
+		p5-SVG>=0:textproc/p5-SVG \
+		p5-SWF-Builder>=0:graphics/p5-SWF-Builder \
+		p5-XML-LibXML>=0:textproc/p5-XML-LibXML \
+		p5-XML-Twig>=0:textproc/p5-XML-Twig \
+		p5-XML-XML2JSON>=0:textproc/p5-XML-XML2JSON \
+		p5-bioperl>=0:biology/p5-bioperl \
+		p5-libxml>=0:textproc/p5-libxml
 RUN_DEPENDS:=	${BUILD_DEPENDS}
-TEST_DEPENDS=	p5-JSON>=0:${PORTSDIR}/converters/p5-JSON
+TEST_DEPENDS=	p5-JSON>=0:converters/p5-JSON
 
 USES=		perl5
 USE_PERL5=	configure
diff --git a/biology/p5-Bio-SCF/Makefile b/biology/p5-Bio-SCF/Makefile
index 7a6d05896f77..c84f76752ca6 100644
--- a/biology/p5-Bio-SCF/Makefile
+++ b/biology/p5-Bio-SCF/Makefile
@@ -11,7 +11,7 @@ PKGNAMEPREFIX=	p5-
 MAINTAINER=	wen@FreeBSD.org
 COMMENT=	Read and Update SCF Chromatographic Sequence Files
 
-BUILD_DEPENDS=	${LOCALBASE}/include/io_lib/scf.h:${PORTSDIR}/biology/iolib
+BUILD_DEPENDS=	${LOCALBASE}/include/io_lib/scf.h:biology/iolib
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 CFLAGS+=	-I${LOCALBASE}/include
diff --git a/biology/p5-bioperl-run/Makefile b/biology/p5-bioperl-run/Makefile
index 711829bbd618..134d8e50d0d1 100644
--- a/biology/p5-bioperl-run/Makefile
+++ b/biology/p5-bioperl-run/Makefile
@@ -13,12 +13,12 @@ COMMENT=	Wrapper modules for common bioinformatics tools
 LICENSE=	ART10 GPLv3
 LICENSE_COMB=	dual
 
-BUILD_DEPENDS=	p5-bioperl>=1.6.0:${PORTSDIR}/biology/p5-bioperl \
-		p5-IPC-Run>=0:${PORTSDIR}/devel/p5-IPC-Run \
-		p5-Algorithm-Diff>=0:${PORTSDIR}/devel/p5-Algorithm-Diff \
-		p5-XML-Twig>=0:${PORTSDIR}/textproc/p5-XML-Twig \
-		p5-File-Sort>=0:${PORTSDIR}/misc/p5-File-Sort \
-		p5-Config-Any>=0:${PORTSDIR}/devel/p5-Config-Any
+BUILD_DEPENDS=	p5-bioperl>=1.6.0:biology/p5-bioperl \
+		p5-IPC-Run>=0:devel/p5-IPC-Run \
+		p5-Algorithm-Diff>=0:devel/p5-Algorithm-Diff \
+		p5-XML-Twig>=0:textproc/p5-XML-Twig \
+		p5-File-Sort>=0:misc/p5-File-Sort \
+		p5-Config-Any>=0:devel/p5-Config-Any
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 CONFLICTS=	p5-bioperl-run-1.[13579]*
diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile
index da1b1d5ed9d2..fd7f623d2668 100644
--- a/biology/p5-bioperl/Makefile
+++ b/biology/p5-bioperl/Makefile
@@ -16,46 +16,46 @@ COMMENT=	Collection of Perl modules for bioinformatics
 LICENSE=	ART10 GPLv1
 LICENSE_COMB=	dual
 
-BUILD_DEPENDS=	p5-Algorithm-Munkres>=0:${PORTSDIR}/math/p5-Algorithm-Munkres \
-		p5-Array-Compare>=0:${PORTSDIR}/misc/p5-Array-Compare \
-		p5-Class-AutoClass>=0:${PORTSDIR}/devel/p5-Class-AutoClass \
-		p5-Clone>=0:${PORTSDIR}/devel/p5-Clone \
-		p5-Convert-Binary-C>=0:${PORTSDIR}/converters/p5-Convert-Binary-C \
-		p5-Data-Stag>=0:${PORTSDIR}/devel/p5-Data-Stag \
-		p5-DBD-mysql>=0:${PORTSDIR}/databases/p5-DBD-mysql \
-		p5-Error>=0:${PORTSDIR}/lang/p5-Error \
-		p5-GD>=0:${PORTSDIR}/graphics/p5-GD \
-		p5-GD-SVG>=0:${PORTSDIR}/graphics/p5-GD-SVG \
-		p5-Graph>=0:${PORTSDIR}/math/p5-Graph \
-		p5-GraphViz>=0:${PORTSDIR}/graphics/p5-GraphViz \
-		p5-HTML-Parser>=0:${PORTSDIR}/www/p5-HTML-Parser \
-		p5-HTML-TableExtract>=2:${PORTSDIR}/www/p5-HTML-TableExtract \
-		p5-IO-stringy>=0:${PORTSDIR}/devel/p5-IO-stringy \
-		p5-IO-String>=0:${PORTSDIR}/devel/p5-IO-String \
-		p5-Math-Random>=0:${PORTSDIR}/math/p5-Math-Random \
-		p5-PostScript>=0:${PORTSDIR}/print/p5-PostScript \
-		p5-SOAP-Lite>=0:${PORTSDIR}/net/p5-SOAP-Lite \
-		p5-Set-Scalar>=0:${PORTSDIR}/devel/p5-Set-Scalar \
-		p5-Sort-Naturally>=1:${PORTSDIR}/textproc/p5-Sort-Naturally \
-		p5-Spreadsheet-ParseExcel>=0:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \
-		p5-SVG>=0:${PORTSDIR}/textproc/p5-SVG \
-		p5-SVG-Graph>=0:${PORTSDIR}/graphics/p5-SVG-Graph \
-		p5-Test-Most>=0:${PORTSDIR}/devel/p5-Test-Most \
-		p5-Text-Shellwords>=0:${PORTSDIR}/textproc/p5-Text-Shellwords \
-		p5-Text-Tabs+Wrap>=0:${PORTSDIR}/textproc/p5-Text-Tabs+Wrap \
-		p5-URI>=0:${PORTSDIR}/net/p5-URI \
-		p5-XML-DOM>=0:${PORTSDIR}/textproc/p5-XML-DOM \
-		p5-XML-DOM-XPath>=0:${PORTSDIR}/textproc/p5-XML-DOM-XPath \
-		p5-XML-LibXML>=0:${PORTSDIR}/textproc/p5-XML-LibXML \
-		p5-XML-Parser>=0:${PORTSDIR}/textproc/p5-XML-Parser \
-		p5-XML-SAX>=0:${PORTSDIR}/textproc/p5-XML-SAX \
-		p5-XML-SAX-Writer>=0:${PORTSDIR}/textproc/p5-XML-SAX-Writer \
-		p5-XML-Simple>=2:${PORTSDIR}/textproc/p5-XML-Simple \
-		p5-XML-Twig>=0:${PORTSDIR}/textproc/p5-XML-Twig \
-		p5-XML-Writer>=0:${PORTSDIR}/textproc/p5-XML-Writer \
-		p5-YAML>=0:${PORTSDIR}/textproc/p5-YAML \
-		p5-libwww>=0:${PORTSDIR}/www/p5-libwww \
-		p5-libxml>=0:${PORTSDIR}/textproc/p5-libxml
+BUILD_DEPENDS=	p5-Algorithm-Munkres>=0:math/p5-Algorithm-Munkres \
+		p5-Array-Compare>=0:misc/p5-Array-Compare \
+		p5-Class-AutoClass>=0:devel/p5-Class-AutoClass \
+		p5-Clone>=0:devel/p5-Clone \
+		p5-Convert-Binary-C>=0:converters/p5-Convert-Binary-C \
+		p5-Data-Stag>=0:devel/p5-Data-Stag \
+		p5-DBD-mysql>=0:databases/p5-DBD-mysql \
+		p5-Error>=0:lang/p5-Error \
+		p5-GD>=0:graphics/p5-GD \
+		p5-GD-SVG>=0:graphics/p5-GD-SVG \
+		p5-Graph>=0:math/p5-Graph \
+		p5-GraphViz>=0:graphics/p5-GraphViz \
+		p5-HTML-Parser>=0:www/p5-HTML-Parser \
+		p5-HTML-TableExtract>=2:www/p5-HTML-TableExtract \
+		p5-IO-stringy>=0:devel/p5-IO-stringy \
+		p5-IO-String>=0:devel/p5-IO-String \
+		p5-Math-Random>=0:math/p5-Math-Random \
+		p5-PostScript>=0:print/p5-PostScript \
+		p5-SOAP-Lite>=0:net/p5-SOAP-Lite \
+		p5-Set-Scalar>=0:devel/p5-Set-Scalar \
+		p5-Sort-Naturally>=1:textproc/p5-Sort-Naturally \
+		p5-Spreadsheet-ParseExcel>=0:textproc/p5-Spreadsheet-ParseExcel \
+		p5-SVG>=0:textproc/p5-SVG \
+		p5-SVG-Graph>=0:graphics/p5-SVG-Graph \
+		p5-Test-Most>=0:devel/p5-Test-Most \
+		p5-Text-Shellwords>=0:textproc/p5-Text-Shellwords \
+		p5-Text-Tabs+Wrap>=0:textproc/p5-Text-Tabs+Wrap \
+		p5-URI>=0:net/p5-URI \
+		p5-XML-DOM>=0:textproc/p5-XML-DOM \
+		p5-XML-DOM-XPath>=0:textproc/p5-XML-DOM-XPath \
+		p5-XML-LibXML>=0:textproc/p5-XML-LibXML \
+		p5-XML-Parser>=0:textproc/p5-XML-Parser \
+		p5-XML-SAX>=0:textproc/p5-XML-SAX \
+		p5-XML-SAX-Writer>=0:textproc/p5-XML-SAX-Writer \
+		p5-XML-Simple>=2:textproc/p5-XML-Simple \
+		p5-XML-Twig>=0:textproc/p5-XML-Twig \
+		p5-XML-Writer>=0:textproc/p5-XML-Writer \
+		p5-YAML>=0:textproc/p5-YAML \
+		p5-libwww>=0:www/p5-libwww \
+		p5-libxml>=0:textproc/p5-libxml
 
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
@@ -66,10 +66,10 @@ NO_ARCH=	yes
 OPTIONS_DEFINE=	DOCS EXAMPLES PGTEST SQLITETEST
 PGTEST_DESC=	Test PostGreSQL
 SQLITETEST_DESC=	Test SQLite
-PGTEST_RUN_DEPENDS=	p5-DBD-Pg>=3:${PORTSDIR}/databases/p5-DBD-Pg
-PGTEST_BUILD_DEPENDS=	p5-DBD-Pg>=3:${PORTSDIR}/databases/p5-DBD-Pg
-SQLITETEST_RUN_DEPENDS=	p5-DBD-SQLite>=1:${PORTSDIR}/databases/p5-DBD-SQLite
-SQLITETEST_BUILD_DEPENDS=	p5-DBD-SQLite>=1:${PORTSDIR}/databases/p5-DBD-SQLite
+PGTEST_RUN_DEPENDS=	p5-DBD-Pg>=3:databases/p5-DBD-Pg
+PGTEST_BUILD_DEPENDS=	p5-DBD-Pg>=3:databases/p5-DBD-Pg
+SQLITETEST_RUN_DEPENDS=	p5-DBD-SQLite>=1:databases/p5-DBD-SQLite
+SQLITETEST_BUILD_DEPENDS=	p5-DBD-SQLite>=1:databases/p5-DBD-SQLite
 
 post-patch:
 	@${FIND} ${WRKSRC}/examples ${WRKSRC}/doc -name "*.pl" -o -name "*.cgi" \
diff --git a/biology/p5-transdecoder/Makefile b/biology/p5-transdecoder/Makefile
index fc0f578bf8a1..003ec621d474 100644
--- a/biology/p5-transdecoder/Makefile
+++ b/biology/p5-transdecoder/Makefile
@@ -12,8 +12,8 @@ COMMENT=	Identify candidate coding regions within transcript sequences
 
 LICENSE=	BSD3CLAUSE
 
-RUN_DEPENDS=	cd-hit>=4.6.1:${PORTSDIR}/biology/cd-hit \
-		p5-URI>0:${PORTSDIR}/net/p5-URI
+RUN_DEPENDS=	cd-hit>=4.6.1:biology/cd-hit \
+		p5-URI>0:net/p5-URI
 
 NO_BUILD=	yes
 NO_ARCH=	yes
diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile
index 7bf26844c122..cb33948fb206 100644
--- a/biology/phylip/Makefile
+++ b/biology/phylip/Makefile
@@ -13,7 +13,7 @@ COMMENT=	Phylogeny Inference Package
 LICENSE=	BSD2CLAUSE
 LICENSE_FILE=	${WRKSRC}/src/COPYRIGHT
 
-BUILD_DEPENDS=	bash:${PORTSDIR}/shells/bash
+BUILD_DEPENDS=	bash:shells/bash
 
 BUILD_WRKSRC=	${WRKSRC}/src
 INSTALL_WRKSRC=	${WRKSRC}/src
diff --git a/biology/phyml/Makefile b/biology/phyml/Makefile
index 4d512f5145dc..3870444c51ac 100644
--- a/biology/phyml/Makefile
+++ b/biology/phyml/Makefile
@@ -28,9 +28,9 @@ OPTIONS_DEFINE=		DOCS EXAMPLES
 OPTIONS_RADIO=		MPI
 OPTIONS_RADIO_MPI=	MPICH2 OPENMPI
 
-MPICH2_LIB_DEPENDS=	libmpich.so:${PORTSDIR}/net/mpich2
+MPICH2_LIB_DEPENDS=	libmpich.so:net/mpich2
 MPICH2_MAKE_ARGS=	CC="${LOCALBASE}/bin/mpicc"
-OPENMPI_LIB_DEPENDS=	libmpi.so:${PORTSDIR}/net/openmpi
+OPENMPI_LIB_DEPENDS=	libmpi.so:net/openmpi
 OPENMPI_MAKE_ARGS=	CC="${LOCALBASE}/mpi/openmpi/bin/mpicc"
 
 .include <bsd.port.options.mk>
diff --git a/biology/plink/Makefile b/biology/plink/Makefile
index 6d4f58deff27..3e6be38a458c 100644
--- a/biology/plink/Makefile
+++ b/biology/plink/Makefile
@@ -13,7 +13,7 @@ COMMENT=	Whole genome association analysis toolset
 
 LICENSE=	GPLv2
 
-LIB_DEPENDS=	liblapack.so:${PORTSDIR}/math/lapack
+LIB_DEPENDS=	liblapack.so:math/lapack
 
 # We need Fortran LDFLAGS to link with Lapack.
 USES=		fortran gmake zip
diff --git a/biology/protomol/Makefile b/biology/protomol/Makefile
index 5710363231cf..c7483b1cf158 100644
--- a/biology/protomol/Makefile
+++ b/biology/protomol/Makefile
@@ -14,8 +14,8 @@ COMMENT=	OO, component based, framework for molecular dynamics (MD) simulations
 LICENSE=	GPLv2
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-LIB_DEPENDS=	libpng.so:${PORTSDIR}/graphics/png \
-		libtiff.so:${PORTSDIR}/graphics/tiff
+LIB_DEPENDS=	libpng.so:graphics/png \
+		libtiff.so:graphics/tiff
 
 USES=		shebangfix
 SHEBANG_FILES=	examples/butane_4/procDihedralFile.awk \
diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
index 197bb328ed97..27f2abdb61e4 100644
--- a/biology/py-biopython/Makefile
+++ b/biology/py-biopython/Makefile
@@ -21,6 +21,6 @@ OPTIONS_DEFINE=	REPORTLAB
 OPTIONS_DEFAULT=	REPORTLAB
 
 REPORTLAB_DESC=	PDF support in Bio.Graphics module
-REPORTLAB_RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}reportlab1>0:${PORTSDIR}/print/py-reportlab1
+REPORTLAB_RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}reportlab1>0:print/py-reportlab1
 
 .include <bsd.port.mk>
diff --git a/biology/pycogent/Makefile b/biology/pycogent/Makefile
index 4d4b6e57f877..1dd650abc285 100644
--- a/biology/pycogent/Makefile
+++ b/biology/pycogent/Makefile
@@ -15,9 +15,9 @@ COMMENT=	Toolkit for statistical analysis of biological sequences
 LICENSE=	GPLv2
 
 BUILD_DEPENDS=	${PYNUMPY} \
-		${LOCALBASE}/bin/cython:${PORTSDIR}/lang/cython \
-		${LOCALBASE}/bin/sphinx-build:${PORTSDIR}/textproc/py-sphinx \
-		${PYTHON_PKGNAMEPREFIX}sqlalchemy06>=0.5:${PORTSDIR}/databases/py-sqlalchemy06
+		${LOCALBASE}/bin/cython:lang/cython \
+		${LOCALBASE}/bin/sphinx-build:textproc/py-sphinx \
+		${PYTHON_PKGNAMEPREFIX}sqlalchemy06>=0.5:databases/py-sqlalchemy06
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 USES=		python
diff --git a/biology/ruby-bio/Makefile b/biology/ruby-bio/Makefile
index 1f06ce5f639d..cff4fc5927b8 100644
--- a/biology/ruby-bio/Makefile
+++ b/biology/ruby-bio/Makefile
@@ -29,10 +29,10 @@ USE_RUBY_SETUP=	yes
 SHEBANG_FILES=	sample/biofetch.rb
 ruby_OLD_CMD=	/usr/proj/bioruby/bin/ruby
 
-XMLPARSER_RUN_DEPENDS=	${RUBY_SITEARCHLIBDIR}/xmlparser.so:${PORTSDIR}/textproc/ruby-xmlparser
-BDB4_RUN_DEPENDS=	${RUBY_SITEARCHLIBDIR}/bdb.so:${PORTSDIR}/databases/ruby-bdb
-MYSQL_RUN_DEPENDS=	rubygem-dbd-mysql>=0:${PORTSDIR}/databases/rubygem-dbd-mysql
-PGSQL_RUN_DEPENDS=	rubygem-dbd-pg>=0:${PORTSDIR}/databases/rubygem-dbd-pg
+XMLPARSER_RUN_DEPENDS=	${RUBY_SITEARCHLIBDIR}/xmlparser.so:textproc/ruby-xmlparser
+BDB4_RUN_DEPENDS=	${RUBY_SITEARCHLIBDIR}/bdb.so:databases/ruby-bdb
+MYSQL_RUN_DEPENDS=	rubygem-dbd-mysql>=0:databases/rubygem-dbd-mysql
+PGSQL_RUN_DEPENDS=	rubygem-dbd-pg>=0:databases/rubygem-dbd-pg
 
 post-patch:
 	${RUBY} -i -pe 'gsub(%r"(/etc/bioinformatics/)") { "${PREFIX}" + $$1 }' \
diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile
index 1be0a2087e47..620026bdf6c7 100644
--- a/biology/samtools/Makefile
+++ b/biology/samtools/Makefile
@@ -11,9 +11,9 @@ COMMENT=	Tools for manipulating next-generation sequencing data
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-BUILD_DEPENDS=	htslib>=1.3:${PORTSDIR}/biology/htslib
-LIB_DEPENDS=	libhts.so:${PORTSDIR}/biology/htslib
-TEST_DEPENDS=	bash:${PORTSDIR}/shells/bash
+BUILD_DEPENDS=	htslib>=1.3:biology/htslib
+LIB_DEPENDS=	libhts.so:biology/htslib
+TEST_DEPENDS=	bash:shells/bash
 
 USE_GITHUB=	yes
 
diff --git a/biology/seaview/Makefile b/biology/seaview/Makefile
index 62c137d5a918..c5d4e6dae278 100644
--- a/biology/seaview/Makefile
+++ b/biology/seaview/Makefile
@@ -15,8 +15,8 @@ BROKEN=		checksum mismatch
 
 LICENSE=	GPLv3
 
-LIB_DEPENDS=	libfltk.so:${PORTSDIR}/x11-toolkits/fltk \
-		libpng.so:${PORTSDIR}/graphics/png
+LIB_DEPENDS=	libfltk.so:x11-toolkits/fltk \
+		libpng.so:graphics/png
 
 WRKSRC=		${WRKDIR}/${PORTNAME}
 
diff --git a/biology/seqtools/Makefile b/biology/seqtools/Makefile
index 6a26778e82ad..57969ce0bc80 100644
--- a/biology/seqtools/Makefile
+++ b/biology/seqtools/Makefile
@@ -10,8 +10,8 @@ COMMENT=	Tools for visualising sequence alignments
 
 LICENSE=	GPLv3
 
-LIB_DEPENDS=	libcurl.so:${PORTSDIR}/ftp/curl \
-		libsqlite3.so:${PORTSDIR}/databases/sqlite3
+LIB_DEPENDS=	libcurl.so:ftp/curl \
+		libsqlite3.so:databases/sqlite3
 
 USES=		execinfo libtool pkgconfig
 GNU_CONFIGURE=	yes
diff --git a/biology/t_coffee/Makefile b/biology/t_coffee/Makefile
index ba3cffaee2c0..c79244ebfe64 100644
--- a/biology/t_coffee/Makefile
+++ b/biology/t_coffee/Makefile
@@ -14,7 +14,7 @@ COMMENT=	Multiple DNA or protein sequence alignment package
 
 LICENSE=	GPLv2
 
-RUN_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw
+RUN_DEPENDS=	clustalw:biology/clustalw
 
 OPTIONS_DEFINE=	EXAMPLES
 
diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile
index 55aab14861c3..88a5dfa468ea 100644
--- a/biology/ugene/Makefile
+++ b/biology/ugene/Makefile
@@ -16,7 +16,7 @@ COMMENT=	Free, open-source, cross-platform bioinformatics toolkit
 
 LICENSE=	GPLv2
 
-RUN_DEPENDS=	bash:${PORTSDIR}/shells/bash
+RUN_DEPENDS=	bash:shells/bash
 
 USES=		desktop-file-utils execinfo qmake
 USE_GL=		glu