Remove FETCH_USING, separate multiple variable assignments, remove some cruft

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: Remove FETCH_USING, separate multiple variable assignments, remove some cruft
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Wed, 11 May 2016 22:47:23 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 17:47:23 2016 -0500
Changeset:	27635364553a5d46f0217ee32627263c882b24ae

Modified Files:
	bamtools/Makefile
	bedtools2/Makefile
	bowtie2/Makefile
	cherokee/Makefile
	cufflinks/Makefile
	fastool/Makefile
	filevercmp/Makefile
	gtextutils/Makefile
	htslib/Makefile
	p5-transdecoder/Makefile
	py-htseq/Makefile
	rsem/Makefile
	samtools/Makefile
	scythe/Makefile
	seqtk/Makefile
	sickle/Makefile
	tophat/Makefile
	trinity/Makefile
	vcftools/Makefile

Log Message:
Remove FETCH_USING, separate multiple variable assignments, remove some cruft

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=27635364553a5d46f0217ee32627263c882b24ae

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 bamtools/Makefile        | 26 +-------------------------
 bedtools2/Makefile       |  2 --
 bowtie2/Makefile         |  2 --
 cherokee/Makefile        |  4 ----
 cufflinks/Makefile       | 46 +++++++++++++++++++++++-----------------------
 fastool/Makefile         |  2 --
 filevercmp/Makefile      |  2 --
 gtextutils/Makefile      |  2 --
 htslib/Makefile          |  2 --
 p5-transdecoder/Makefile |  2 --
 py-htseq/Makefile        |  3 ---
 rsem/Makefile            |  2 --
 samtools/Makefile        |  2 --
 scythe/Makefile          |  2 --
 seqtk/Makefile           |  2 --
 sickle/Makefile          |  2 --
 tophat/Makefile          | 10 +++++-----
 trinity/Makefile         | 24 +++++++++++-------------
 vcftools/Makefile        |  2 --
 19 files changed, 40 insertions(+), 99 deletions(-)

diffs:
diff --git a/bamtools/Makefile b/bamtools/Makefile
index 03ee035..e3b4d23 100644
--- a/bamtools/Makefile
+++ b/bamtools/Makefile
@@ -7,12 +7,8 @@
 ###########################################################
 # Unconverted and partially converted FreeBSD port syntax:
 
-# # Created by: Dan Siercks
-# # $FreeBSD$
 # Unknown tool: USE_TOOLS=	cmake:outsource
-# USE_LDCONFIG=	yes
 # CMAKE_ARGS+=	-DLIB_DIR=${PREFIX}/lib
-# .include <bsd.port.pre.mk>
 # # Just for speed: Recent compilers have better optimizers
 # Unknown tool: USE_TOOLS=	compiler:c++11-lang
 # .if ${ARCH} == i386
@@ -21,7 +17,6 @@
 # post-patch:
 # 	${REINPLACE_CMD} -e 's|lib/bamtools|lib|g' \
 # 		work/bamtools-2.4.0/src/api/CMakeLists.txt
-# .include <bsd.port.post.mk>
 
 DISTNAME=	bamtools-${PORTVERSION}
 CATEGORIES=	biology
@@ -34,9 +29,6 @@ COMMENT=	API and toolkit for handling BAM files
 # Double-check this
 LICENSE=	mit
 
-# Test and change if necessary.
-# MAKE_JOBS_SAFE=	no
-
 # Just assuming C and C++: Adjust this!
 USE_CMAKE=	yes
 USE_LANGUAGES=	c c++
@@ -46,11 +38,9 @@ CONFIGURE_DIRS=	_build
 pre-configure:
 	${MKDIR} ${WRKSRC}/_build
 
-
 WRKSRC=		${WRKDIR}/bamtools-${PORTVERSION}
 
-# Adapt REINPLACE commands to SUBST:
-SUBST_CLASSES+= bamtools_lib
+SUBST_CLASSES+=			bamtools_lib
 SUBST_STAGE.bamtools_lib=	post-patch
 SUBST_FILES.bamtools_lib=	${WRKSRC}/src/api/CMakeLists.txt
 SUBST_SED.bamtools_lib=		-e 's|lib/bamtools|lib|g'
@@ -60,21 +50,7 @@ SUBST_SED.bamtools_lib=		-e 's|lib/bamtools|lib|g'
 #SUBST_FILES.bluetooth=	${WRKSRC}/Commands/Legoctl/Makefile
 #SUBST_SED.bluetooth=	-e 's|-lbluetooth||g'
 
-FETCH_USING=	curl
-
 PORTVERSION=	2.4.0
-#DATADIR=	${PREFIX}/share/bamtools
-#DOCSDIR=	${PREFIX}/share/doc/bamtools
-
-# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
-# .include "../../mk/bsd.prefs.mk"
-
-# Keep this if there are user-selectable options.
-# .include "options.mk"
-
-# Specify which directories to create before install.
-# INSTALLATION_DIRS=	bin lib ${PKGMANDIR}/man1 share/doc share/examples
 
-# Linux doesn't have zlib in the base, so just in case...
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/bedtools2/Makefile b/bedtools2/Makefile
index 4bb2d5a..429c142 100644
--- a/bedtools2/Makefile
+++ b/bedtools2/Makefile
@@ -31,8 +31,6 @@ WRKSRC=		${WRKDIR}/bedtools2-${PORTVERSION}
 
 MAKE_ENV=	PYTHONBIN=${PYTHONBIN}
 
-FETCH_USING=	curl
-
 PORTVERSION=	2.23.0
 
 .include "../../devel/zlib/buildlink3.mk"
diff --git a/bowtie2/Makefile b/bowtie2/Makefile
index 14e24e8..bd08129 100644
--- a/bowtie2/Makefile
+++ b/bowtie2/Makefile
@@ -21,8 +21,6 @@ USE_TOOLS+=	gmake perl:run pax
 REPLACE_PERL=	scripts/*.pl bowtie2
 REPLACE_PYTHON=	bowtie2-build bowtie2-inspect
 
-FETCH_USING=	curl
-
 PORTVERSION=	2.2.7
 DATADIR=	${PREFIX}/share/bowtie2
 DOCSDIR=	${PREFIX}/share/doc/bowtie2
diff --git a/cherokee/Makefile b/cherokee/Makefile
index 6e35fe4..58d8f96 100644
--- a/cherokee/Makefile
+++ b/cherokee/Makefile
@@ -16,10 +16,6 @@ LICENSE=	gnu-gpl-v2
 WRKSRC=		${WRKDIR}/webserver-${GIT_COMMIT}
 PKG_DESTDIR_SUPPORT=	user-destdir
 
-# Force using "curl" for fetching the distribution file. It is only available
-# over HTTPS and "curl" is the only fetch program which always supports HTTPS.
-FETCH_USING=    curl
-
 GNU_CONFIGURE=		yes
 USE_LIBTOOL=		yes
 USE_TOOLS+=		autoconf automake gmake gm4 msgfmt
diff --git a/cufflinks/Makefile b/cufflinks/Makefile
index 8602955..14a3d50 100644
--- a/cufflinks/Makefile
+++ b/cufflinks/Makefile
@@ -31,29 +31,29 @@ SUBST_SED.boost+=	-e 's|long double|double|g'
 SUBST_SED.boost+=	-e 's|Lf|lf|g'
 SUBST_SED.boost+=	-e 's|Lg|lg|g'
 SUBST_MESSAGE.boost=	"Substituting for boost"
-SUBST_FILES.boost=	${WRKSRC}/src/abundances.cpp \
-			${WRKSRC}/src/abundances.h \
-			${WRKSRC}/src/assemble.h \
-			${WRKSRC}/src/biascorrection.cpp \
-			${WRKSRC}/src/biascorrection.h \
-			${WRKSRC}/src/bundles.cpp \
-			${WRKSRC}/src/bundles.cpp.orig \
-			${WRKSRC}/src/bundles.h \
-			${WRKSRC}/src/clustering.cpp \
-			${WRKSRC}/src/common.h \
-			${WRKSRC}/src/compress_gtf.cpp \
-			${WRKSRC}/src/cuffdiff.cpp \
-			${WRKSRC}/src/cufflinks.cpp \
-			${WRKSRC}/src/differential.cpp \
-			${WRKSRC}/src/differential.h \
-			${WRKSRC}/src/filters.cpp \
-			${WRKSRC}/src/filters.h \
-			${WRKSRC}/src/gtf_to_sam.cpp \
-			${WRKSRC}/src/hits.h \
-			${WRKSRC}/src/replicates.cpp \
-			${WRKSRC}/src/replicates.h \
-			${WRKSRC}/src/scaffolds.cpp \
-			${WRKSRC}/src/scaffolds.h
+SUBST_FILES.boost+=	${WRKSRC}/src/abundances.cpp
+SUBST_FILES.boost+=	${WRKSRC}/src/abundances.h
+SUBST_FILES.boost+=	${WRKSRC}/src/assemble.h
+SUBST_FILES.boost+=	${WRKSRC}/src/biascorrection.cpp
+SUBST_FILES.boost+=	${WRKSRC}/src/biascorrection.h
+SUBST_FILES.boost+=	${WRKSRC}/src/bundles.cpp
+SUBST_FILES.boost+=	${WRKSRC}/src/bundles.cpp.orig
+SUBST_FILES.boost+=	${WRKSRC}/src/bundles.h
+SUBST_FILES.boost+=	${WRKSRC}/src/clustering.cpp
+SUBST_FILES.boost+=	${WRKSRC}/src/common.h
+SUBST_FILES.boost+=	${WRKSRC}/src/compress_gtf.cpp
+SUBST_FILES.boost+=	${WRKSRC}/src/cuffdiff.cpp
+SUBST_FILES.boost+=	${WRKSRC}/src/cufflinks.cpp
+SUBST_FILES.boost+=	${WRKSRC}/src/differential.cpp
+SUBST_FILES.boost+=	${WRKSRC}/src/differential.h
+SUBST_FILES.boost+=	${WRKSRC}/src/filters.cpp
+SUBST_FILES.boost+=	${WRKSRC}/src/filters.h
+SUBST_FILES.boost+=	${WRKSRC}/src/gtf_to_sam.cpp
+SUBST_FILES.boost+=	${WRKSRC}/src/hits.h
+SUBST_FILES.boost+=	${WRKSRC}/src/replicates.cpp
+SUBST_FILES.boost+=	${WRKSRC}/src/replicates.h
+SUBST_FILES.boost+=	${WRKSRC}/src/scaffolds.cpp
+SUBST_FILES.boost+=	${WRKSRC}/src/scaffolds.h
 
 SUBST_CLASSES+=		boolint
 SUBST_STAGE.boolint=	post-patch
diff --git a/fastool/Makefile b/fastool/Makefile
index 03d6648..39251fe 100644
--- a/fastool/Makefile
+++ b/fastool/Makefile
@@ -25,8 +25,6 @@ SUBST_SED.compiler=	-e 's|CFLAGS *=|CFLAGS ?=|g'
 
 CFLAGS+=	-std=c99
 
-FETCH_USING=	curl
-
 PORTVERSION=	0.1.4
 
 INSTALLATION_DIRS=	bin
diff --git a/filevercmp/Makefile b/filevercmp/Makefile
index a6c959e..525f6ff 100644
--- a/filevercmp/Makefile
+++ b/filevercmp/Makefile
@@ -16,6 +16,4 @@ LICENSE=	gnu-gpl-v3
 
 PORTVERSION=	261142f1529f6b7464f6ad96d0c77872ff919849
 
-FETCH_USING=	curl
-
 .include "../../mk/bsd.pkg.mk"
diff --git a/gtextutils/Makefile b/gtextutils/Makefile
index 23f5e47..cd4e17b 100644
--- a/gtextutils/Makefile
+++ b/gtextutils/Makefile
@@ -17,6 +17,4 @@ USE_LANGUAGES=	c c++
 USE_TOOLS+=	 pkg-config
 GNU_CONFIGURE=	yes
 
-FETCH_USING=	curl
-
 .include "../../mk/bsd.pkg.mk"
diff --git a/htslib/Makefile b/htslib/Makefile
index deb1353..9c6efc5 100644
--- a/htslib/Makefile
+++ b/htslib/Makefile
@@ -52,8 +52,6 @@ MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
 		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
 		INSTALL_DIR="${MKDIR}"
 
-FETCH_USING=	curl
-
 PORTVERSION=	1.3
 SITE_PERL=	${PREFIX}/share
 DATADIR=	${PREFIX}/share/htslib
diff --git a/p5-transdecoder/Makefile b/p5-transdecoder/Makefile
index 3b9955e..62ab436 100644
--- a/p5-transdecoder/Makefile
+++ b/p5-transdecoder/Makefile
@@ -36,8 +36,6 @@ REPLACE_PERL=	util/*.pl sample_data/*.pl PerlLib/*.pm \
 		TransDecoder.LongOrfs TransDecoder.Predict
 NO_BUILD=	yes
 
-FETCH_USING=	curl
-
 PORTVERSION=	2.0.1
 
 INSTALLATION_DIRS=	bin lib/TransDecoder/PerlLib libexec/TransDecoder/util
diff --git a/py-htseq/Makefile b/py-htseq/Makefile
index 6c53422..0f20dbe 100644
--- a/py-htseq/Makefile
+++ b/py-htseq/Makefile
@@ -16,13 +16,10 @@ LICENSE=	gnu-gpl-v3
 
 # Just assuming C and C++: Adjust this!
 USE_LANGUAGES=	c c++
-PYDISTUTILSPKG=	yes
 
 PORTVERSION=	0.6.1p1
 MASTER_SITE_CHEESESHOP= http://pypi.python.org/packages
 
-FETCH_USING=	curl
-
 .include "../../lang/python/distutils.mk"
 .include "../../math/py-numpy/buildlink3.mk"
 .include "../../graphics/py-matplotlib/buildlink3.mk"
diff --git a/rsem/Makefile b/rsem/Makefile
index d607946..1d05f2b 100644
--- a/rsem/Makefile
+++ b/rsem/Makefile
@@ -61,8 +61,6 @@ WRKSRC=		${WRKDIR}/RSEM-${PORTVERSION}
 MAKE_ENV=	libexecdir=${PREFIX}/libexec \
 		perl_mod_dir=${SITE_PERL}
 
-FETCH_USING=	curl
-
 PORTVERSION=	1.2.30
 SITE_PERL=	${PREFIX}/share/rsem
 
diff --git a/samtools/Makefile b/samtools/Makefile
index a69aa84..c982cd5 100644
--- a/samtools/Makefile
+++ b/samtools/Makefile
@@ -45,8 +45,6 @@ MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
 		INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
 		INSTALL_DIR="${MKDIR}"
 
-FETCH_USING=	curl
-
 PORTVERSION=	1.3
 SITE_PERL=	${PREFIX}/share
 DATADIR=	${PREFIX}/share/samtools
diff --git a/scythe/Makefile b/scythe/Makefile
index 49b6067..1bbf390 100644
--- a/scythe/Makefile
+++ b/scythe/Makefile
@@ -36,8 +36,6 @@ USE_TOOLS+=	gmake
 
 WRKSRC=		${WRKDIR}/scythe-${GITHUB_TAG}
 
-FETCH_USING=	curl
-
 PORTVERSION=	2016.02.10
 #DATADIR=	${PREFIX}/share/scythe
 #DOCSDIR=	${PREFIX}/share/doc/scythe
diff --git a/seqtk/Makefile b/seqtk/Makefile
index 4b305e0..4877bc6 100644
--- a/seqtk/Makefile
+++ b/seqtk/Makefile
@@ -24,8 +24,6 @@ WRKSRC=		${WRKDIR}/seqtk-${PORTVERSION}
 CFLAGS+=	-msse2
 .endif
 
-FETCH_USING=	curl
-
 PORTVERSION=	4feb6e81444ab6bc44139dd3a125068f81ae4ad8
 
 do-install:
diff --git a/sickle/Makefile b/sickle/Makefile
index c7780f9..5bfcdb5 100644
--- a/sickle/Makefile
+++ b/sickle/Makefile
@@ -36,8 +36,6 @@ LICENSE=	gnu-gpl-v2
 USE_LANGUAGES=	c c++
 USE_TOOLS+=	gmake
 
-FETCH_USING=	curl
-
 PORTVERSION=	1.33
 #DATADIR=	${PREFIX}/share/sickle
 #DOCSDIR=	${PREFIX}/share/doc/sickle
diff --git a/tophat/Makefile b/tophat/Makefile
index ddd1394..54e61df 100644
--- a/tophat/Makefile
+++ b/tophat/Makefile
@@ -23,11 +23,11 @@ USE_LANGUAGES=	c c++
 USE_TOOLS+=	gmake
 GNU_CONFIGURE=	yes
 
-REPLACE_PYTHON=	src/bed_to_juncs \
-		src/contig_to_chr_coords \
-		src/sra_to_solid \
-		src/tophat-fusion-post \
-		src/tophat.py
+REPLACE_PYTHON=	src/bed_to_juncs
+REPLACE_PYTHON=	src/contig_to_chr_coords
+REPLACE_PYTHON=	src/sra_to_solid
+REPLACE_PYTHON=	src/tophat-fusion-post
+REPLACE_PYTHON=	src/tophat.py
 REPLACE_BASH=	src/tophat2.sh
 
 CFLAGS+=	-Wno-unused
diff --git a/trinity/Makefile b/trinity/Makefile
index e46e5a5..edfbd87 100644
--- a/trinity/Makefile
+++ b/trinity/Makefile
@@ -26,17 +26,17 @@
 #JAVA_VERSION=	1.7 1.6
 #		slclust:/usr/wip/biology/slclust
 
-DEPENDS+=	coreutils>=0:../../sysutils/coreutils \
-		bowtie<2:../../wip/bowtie \
-		bowtie2>=2:../../wip/bowtie2 \
-		jellyfish>=2.1.4:../../wip/jellyfish2 \
-		parafly>=0:../../wip/parafly \
-		fastool>=0:../../wip/fastool \
-		p5-transdecoder>=0:../../wip/p5-transdecoder \
-		Trimmomatic>=0.32:../../wip/trimmomatic \
-		rsem>=1.2.30:../../wip/rsem \
-		slclust>=0:../../wip/slclust \
-		samtools>=1.3:../../wip/samtools
+DEPENDS+=	coreutils>=0:../../sysutils/coreutils
+DEPENDS+=	bowtie<2:../../wip/bowtie
+DEPENDS+=	bowtie2>=2:../../wip/bowtie2
+DEPENDS+=	jellyfish>=2.1.4:../../wip/jellyfish2
+DEPENDS+=	parafly>=0:../../wip/parafly
+DEPENDS+=	fastool>=0:../../wip/fastool
+DEPENDS+=	p5-transdecoder>=0:../../wip/p5-transdecoder
+DEPENDS+=	Trimmomatic>=0.32:../../wip/trimmomatic
+DEPENDS+=	rsem>=1.2.30:../../wip/rsem
+DEPENDS+=	slclust>=0:../../wip/slclust
+DEPENDS+=	samtools>=1.3:../../wip/samtools
 
 DISTNAME=	trinity-${PORTVERSION}
 CATEGORIES=	biology
@@ -136,8 +136,6 @@ WRKSRC=		${WRKDIR}/trinityrnaseq-${PORTVERSION}
 CFLAGS+=	-fopenmp
 CXXFLAGS=	-fopenmp
 
-FETCH_USING=	curl
-
 PORTVERSION=	2.1.1
 EXAMPLESDIR=	${PREFIX}/share/examples/trinity
 LIBEXEC_DIR=	${PREFIX}/libexec/trinity
diff --git a/vcftools/Makefile b/vcftools/Makefile
index 2eb5859..3e7b414 100644
--- a/vcftools/Makefile
+++ b/vcftools/Makefile
@@ -25,8 +25,6 @@ REPLACE_PERL=	src/perl/*
 # No zlib.pc on FreeBSD 9.x
 CONFIGURE_ENV=	ZLIB_CFLAGS=" " ZLIB_LIBS="-lz"
 
-FETCH_USING=	curl
-
 PORTVERSION=	0.1.14
 
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