trinity-devel: Test new version before removing old

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: trinity-devel: Test new version before removing old
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Sat, 15 Sep 2018 02:57:57 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Sep 14 21:57:57 2018 -0500
Changeset:	a2a4c70ca631c5b30da8be0630caf318e8f0866a

Modified Files:
	Makefile
Added Files:
	trinity-devel/DESCR
	trinity-devel/Makefile
	trinity-devel/PLIST
	trinity-devel/distinfo
	trinity-devel/patches/patch-Chrysalis_CMakeLists.txt
	trinity-devel/patches/patch-Chrysalis_Makefile
	trinity-devel/patches/patch-Inchworm_CMakeLists.txt
	trinity-devel/patches/patch-Inchworm_Makefile
	trinity-devel/patches/patch-Makefile
	trinity-devel/patches/patch-trinity-plugins_Makefile
	trinity-devel/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
	trinity-devel/patches/patch-util_support__scripts_plugin__install__tests.sh

Log Message:
trinity-devel: Test new version before removing old

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=a2a4c70ca631c5b30da8be0630caf318e8f0866a

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

diffstat:
 Makefile                                           |   1 +
 trinity-devel/DESCR                                |   4 +
 trinity-devel/Makefile                             | 155 +++++++++++++++++++++
 trinity-devel/PLIST                                |   1 +
 trinity-devel/distinfo                             |  14 ++
 .../patches/patch-Chrysalis_CMakeLists.txt         |  13 ++
 trinity-devel/patches/patch-Chrysalis_Makefile     |  21 +++
 .../patches/patch-Inchworm_CMakeLists.txt          |  13 ++
 trinity-devel/patches/patch-Inchworm_Makefile      |  15 ++
 trinity-devel/patches/patch-Makefile               |  13 ++
 .../patches/patch-trinity-plugins_Makefile         |  34 +++++
 ...inity-plugins_scaffold__iworm__contigs_Makefile |  15 ++
 ...util_support__scripts_plugin__install__tests.sh |  13 ++
 13 files changed, 312 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index ced22360b2..2af324ef34 100644
--- a/Makefile
+++ b/Makefile
@@ -4443,6 +4443,7 @@ SUBDIR+=	triforce-afl
 SUBDIR+=	trimadap
 SUBDIR+=	trimmomatic
 SUBDIR+=	trinity
+SUBDIR+=	trinity-devel
 SUBDIR+=	tripwire2
 SUBDIR+=	truecrypt
 SUBDIR+=	tsh
diff --git a/trinity-devel/DESCR b/trinity-devel/DESCR
new file mode 100644
index 0000000000..7752b73aa7
--- /dev/null
+++ b/trinity-devel/DESCR
@@ -0,0 +1,4 @@
+Trinity represents a novel method for the efficient and robust de novo
+reconstruction of transcriptomes from RNA-seq data.  Trinity combines three
+independent software modules: Inchworm, Chrysalis, and Butterfly, applied
+sequentially to process large volumes of RNA-seq reads.
diff --git a/trinity-devel/Makefile b/trinity-devel/Makefile
new file mode 100644
index 0000000000..cae62661b6
--- /dev/null
+++ b/trinity-devel/Makefile
@@ -0,0 +1,155 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Fri Sep 14 20:48:17 CDT 2018               #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+# Trinity core programs: Inchworm, Chrysalis, Butterfly
+# Bundled plugins: Trinity is very sensitive to having the correct versions
+# of some of these.  Test thoroughly if you change any of them.
+# To-do:
+#	Unbundle collectl (low priority)
+## Should work on other 64-bit archs, but untested
+#ONLY_FOR_ARCH=	amd64
+
+# Should salmon use bl3?
+# bowtie should not have bl3
+DEPENDS=	coreutils>=0:../../sysutils/coreutils
+DEPENDS+=	bash>=0:../../shells/bash
+DEPENDS+=	slclust>=0:../../wip/slclust
+DEPENDS+=	salmon>=0:../../wip/salmon
+DEPENDS+=	bowtie>=0:../../wip/bowtie
+DEPENDS+=	bowtie2>=0:../../wip/bowtie2
+DEPENDS+=	samtools>=1.3:../../biology/samtools
+DEPENDS+=	jellyfish>=2.1.4:../../wip/jellyfish
+DEPENDS+=	parafly>=0:../../wip/parafly
+DEPENDS+=	fastool>=0:../../wip/fastool
+DEPENDS+=	p5-transdecoder>=0:../../wip/p5-transdecoder
+DEPENDS+=	Trimmomatic>=0.38:../../wip/trimmomatic
+DEPENDS+=	rsem>=1.2.27:../../wip/rsem
+
+DISTNAME=	trinity-${PV}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=trinityrnaseq/}
+GITHUB_PROJECT=	trinityrnaseq
+GITHUB_TAG=	Trinity-v${PV}
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	http://trinityrnaseq.github.io/
+COMMENT=	Assembles transcript sequences from Illumina RNA-Seq data
+LICENSE=	modified-bsd
+
+# MAKE_JOBS_SAFE=	no
+
+USE_LANGUAGES=	c c++
+USE_JAVA=	run
+USE_TOOLS+=	cmake gmake pax
+USE_CMAKE=	yes
+
+REPLACE_BASH=	util/*/*.sh
+REPLACE_BASH+=	util/misc/alt_GG_read_partitioning_JCornish/genwig.sh
+REPLACE_BASH+=	Analysis/DifferentialExpression/cluster_sample_data/runMe.sh
+REPLACE_PERL=	util/*/*.pl Chrysalis/analysis/*.pl 
+REPLACE_PYTHON=	util/support_scripts/trinity_installer.py
+REPLACE_PYTHON+=util/misc/alt_GG_read_partitioning_JCornish/genwig2.py
+REPLACE_PYTHON+=util/misc/sim_test_framework/run_Trinity_eval.sh
+REPLACE_PYTHON+=util/misc/TPM_weighted_gene_length.py
+REPLACE_PYTHON+=Analysis/SuperTranscripts/*.py
+REPLACE_PYTHON+=Analysis/SuperTranscripts/*/*.py
+
+SUBST_CLASSES+=		compiler
+SUBST_STAGE.compiler=	post-patch
+SUBST_SED.compiler+=	-e "s|gcc|${CC}|g"
+SUBST_SED.compiler+=	-e "s|g++|${CXX}|g"
+SUBST_FILES.compiler+=	${WRKSRC}/Chrysalis/Makefile*
+
+SUBST_CLASSES+=		paths
+SUBST_STAGE.paths=	post-patch
+SUBST_SED.paths+=	-e 's|$$FindBin::Bin|$$FindBin::Bin/../libexec/trinity|g'
+SUBST_SED.paths+=	-e 's|$$FindBin::RealBin|$$FindBin::RealBin/../libexec/trinity|g'
+SUBST_SED.paths+=	-e 's|$$ROOTDIR/trinity-plugins/BIN/ParaFly|ParaFly|g'
+SUBST_SED.paths+=	-e 's|$$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar|${JAVAJARDIR}/trimmomatic.jar|g'
+SUBST_SED.paths+=	-e 's|$$ROOTDIR/trinity-plugins/Trimmomatic|${LOCALBASE}/share/Trimmomatic|g'
+SUBST_FILES.paths+=	${WRKSRC}/Trinity
+
+SUBST_CLASSES+=		jelly
+SUBST_STAGE.jelly=	post-patch
+SUBST_SED.jelly+=	-e 's|$$JELLYFISH_DIR/bin/jellyfish|jellyfish|g'
+SUBST_FILES.jelly+=	${WRKSRC}/util/misc/run_jellyfish.pl
+
+SUBST_CLASSES+=		trimmo
+SUBST_STAGE.trimmo=	post-patch
+SUBST_SED.trimmo+=	-e 's|$$FindBin::RealBin/../../trinity-plugins/Trimmomatic/trimmomatic.jar|${JAVAJARDIR}/trimmomatic.jar|g'
+SUBST_SED.trimmo+=	-e 's|/seq/regev_genome_portal/SOFTWARE/BIN/trimmomatic.jar|${JAVAJARDIR}/trimmomatic.jar|g'
+SUBST_FILES.trimmo+=	${WRKSRC}/util/misc/run_trimmomatic_qual_trimming.pl
+
+SUBST_CLASSES+=		rpath
+SUBST_STAGE.rpath=	post-patch
+SUBST_SED.rpath+=	-e "s|-lm -pthread|-lm -pthread -Wl,-rpath=${_GCC_RUNTIME}|g"
+SUBST_FILES.rpath+=	${WRKSRC}/Chrysalis/Makefile
+
+SUBST_CLASSES+=		trinity
+SUBST_STAGE.trinity=	post-patch
+SUBST_SED.trinity+=	-e 's|$$FindBin::Bin/../../Trinity|Trinity|g'
+SUBST_FILES.trinity+=	${WRKSRC}/util/support_scripts/write_partitioned_trinity_cmds.pl
+
+SUBST_CLASSES+=		build
+SUBST_STAGE.build=	post-build
+SUBST_SED.build+=	-e "s|/usr/bin/perl|${PREFIX}/bin/perl|g"
+SUBST_FILES.build+=	${WRKSRC}/trinity-plugins/COLLECTL/collectl/collectl
+SUBST_FILES.build+=	${WRKSRC}/trinity-plugins/COLLECTL/collectl/*.pl
+
+CFLAGS+=	-fopenmp
+CXXFLAGS=	-fopenmp 
+FFLAGS=		-fopenmp 
+
+PV=		2.8.3
+EXAMPLESDIR=	${PREFIX}/share/examples/trinity
+LIBEXEC_DIR=	${PREFIX}/libexec/trinity
+PLUGINS_DIR=	${LIBEXEC_DIR}/trinity-plugins
+
+# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
+# .include "../../mk/bsd.prefs.mk"
+
+INSTALLATION_DIRS=	bin include lib ${PKGMANDIR}/man1 share/doc share/examples
+
+# FIXME: More may need to be installed
+do-install:
+	${INSTALL_SCRIPT} ${WRKSRC}/Trinity ${DESTDIR}${PREFIX}/bin
+	@${MKDIR} ${DESTDIR}${LIBEXEC_DIR}/Chrysalis/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/Chrysalis/bin/* \
+		${DESTDIR}${LIBEXEC_DIR}/Chrysalis/bin
+	${INSTALL_SCRIPT} ${WRKSRC}/Chrysalis/analysis/ReadsToComponents.pl \
+		${DESTDIR}${LIBEXEC_DIR}/Chrysalis/bin
+	@${MKDIR} ${DESTDIR}${LIBEXEC_DIR}/Inchworm/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/Inchworm/bin/* \
+		${DESTDIR}${LIBEXEC_DIR}/Inchworm/bin
+	@${MKDIR} ${DESTDIR}${LIBEXEC_DIR}/Butterfly
+	${INSTALL_SCRIPT} ${WRKSRC}/Butterfly/Butterfly.jar \
+		${DESTDIR}${LIBEXEC_DIR}/Butterfly
+	cd ${WRKSRC} && pax -rw PerlLib \
+		${DESTDIR}${LIBEXEC_DIR}
+	cd ${WRKSRC} && pax -rw util \
+		${DESTDIR}${LIBEXEC_DIR}
+	cd ${WRKSRC} && pax -rw Analysis \
+		${DESTDIR}${LIBEXEC_DIR}
+	@${MKDIR} ${DESTDIR}${PLUGINS_DIR}/scaffold_iworm_contigs
+	${INSTALL_PROGRAM} ${WRKSRC}/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs \
+		${DESTDIR}${PLUGINS_DIR}/scaffold_iworm_contigs
+	@${MKDIR} ${DESTDIR}${PLUGINS_DIR}/BIN
+	${INSTALL_PROGRAM} ${WRKSRC}/trinity-plugins/BIN/seqtk-trinity \
+		${DESTDIR}${PLUGINS_DIR}/BIN
+	cd ${WRKSRC}/sample_data && pax -rw \* \
+		${DESTDIR}${EXAMPLESDIR}
+	${RLN} ${DESTDIR}${PREFIX}/bin/Trinity \
+		${DESTDIR}${PREFIX}/libexec/trinity/Trinity
+
+.include "../../lang/python/application.mk"
+.include "../../biology/htslib/buildlink3.mk"
+# CentOS doesn't have zlib in the base, so uncomment if needed.
+# .include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/trinity-devel/PLIST b/trinity-devel/PLIST
new file mode 100644
index 0000000000..48d96a5493
--- /dev/null
+++ b/trinity-devel/PLIST
@@ -0,0 +1 @@
+@comment $NetBSD$
diff --git a/trinity-devel/distinfo b/trinity-devel/distinfo
new file mode 100644
index 0000000000..8dacf5ca9e
--- /dev/null
+++ b/trinity-devel/distinfo
@@ -0,0 +1,14 @@
+$NetBSD$
+
+SHA1 (trinity-2.8.3.tar.gz) = e9553095eb526bb478eac8237fae2bab7d143126
+RMD160 (trinity-2.8.3.tar.gz) = 92a7a81b15a220ff70f3ff5cb3fb80617d041c9d
+SHA512 (trinity-2.8.3.tar.gz) = 45f0712b2732591688697d3b4726e3c2f64a507d97f080b1cfeaf2d16647b196b2a3b45aac45640877bb0c4eced8578ca16fc57cd778b7a1c84908c76cee299f
+Size (trinity-2.8.3.tar.gz) = 21707766 bytes
+SHA1 (patch-Chrysalis_CMakeLists.txt) = 55302c3f624581a191e6688e9dee414fb3cc559c
+SHA1 (patch-Chrysalis_Makefile) = d26bd821acc6b70b145eda1c4a406955f6ac7c0e
+SHA1 (patch-Inchworm_CMakeLists.txt) = b0c3a95ab6c12f24985794c6d61ac9619bfb3add
+SHA1 (patch-Inchworm_Makefile) = 4aa9e682648484976e9cc611e2715b7fb9109e45
+SHA1 (patch-Makefile) = 07ca4b2a3f9157b822e9e05cf4f70b437b7fb5de
+SHA1 (patch-trinity-plugins_Makefile) = 173d54aa7a80edc3c429fe145cab841cdf4dca01
+SHA1 (patch-trinity-plugins_scaffold__iworm__contigs_Makefile) = e946e46209d0654c285f829017e5753eb3444fa0
+SHA1 (patch-util_support__scripts_plugin__install__tests.sh) = 5da1d3872d6632ffb33a84f4cd4ee57c367130f3
diff --git a/trinity-devel/patches/patch-Chrysalis_CMakeLists.txt b/trinity-devel/patches/patch-Chrysalis_CMakeLists.txt
new file mode 100644
index 0000000000..dd6a5f0416
--- /dev/null
+++ b/trinity-devel/patches/patch-Chrysalis_CMakeLists.txt
@@ -0,0 +1,13 @@
+$NetBSD$
+
+--- Chrysalis/CMakeLists.txt.orig	2018-09-01 15:19:53 UTC
++++ Chrysalis/CMakeLists.txt
+@@ -18,7 +18,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} 
+ set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O2 -march=native -DNDEBUG ")
+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g -O0")
+ 
+-set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lm -ldl ")
++set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lm ")
+ 
+ MESSAGE(STATUS "system: ${CMAKE_SYSTEM_NAME}")
+ if (${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
diff --git a/trinity-devel/patches/patch-Chrysalis_Makefile b/trinity-devel/patches/patch-Chrysalis_Makefile
new file mode 100644
index 0000000000..d9e215adc7
--- /dev/null
+++ b/trinity-devel/patches/patch-Chrysalis_Makefile
@@ -0,0 +1,21 @@
+$NetBSD$
+
+--- Chrysalis/Makefile.orig	2018-09-01 15:20:04 UTC
++++ Chrysalis/Makefile
+@@ -1,13 +1,13 @@
+ all:
+ 	mkdir -p build
+-	cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install
++	cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && ${MAKE} DESTDIR=../ install
+ 
+ debug:
+ 	mkdir -p build
+-	cd build && cmake -DCMAKE_INSTALL_PREFIX="" -DCMAKE_BUILD_TYPE=Debug ../ && make DESTDIR=../ install
++	cd build && cmake -DCMAKE_INSTALL_PREFIX="" -DCMAKE_BUILD_TYPE=Debug ../ && ${MAKE} DESTDIR=../ install
+ 
+ 
+ clean:
+ 	@echo cleaning
+-	(cd build && make clean) || :
++	(cd build && ${MAKE} clean) || :
+ 	rm -rf ./build ./bin
diff --git a/trinity-devel/patches/patch-Inchworm_CMakeLists.txt b/trinity-devel/patches/patch-Inchworm_CMakeLists.txt
new file mode 100644
index 0000000000..5136908481
--- /dev/null
+++ b/trinity-devel/patches/patch-Inchworm_CMakeLists.txt
@@ -0,0 +1,13 @@
+$NetBSD$
+
+--- Inchworm/CMakeLists.txt.orig	2018-09-01 15:19:04 UTC
++++ Inchworm/CMakeLists.txt
+@@ -18,7 +18,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} 
+ set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O2 -march=native -DNDEBUG ")
+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g -O0")
+ 
+-set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lm -ldl ")
++set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lm ")
+ 
+ MESSAGE(STATUS "system: ${CMAKE_SYSTEM_NAME}")
+ if (${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
diff --git a/trinity-devel/patches/patch-Inchworm_Makefile b/trinity-devel/patches/patch-Inchworm_Makefile
new file mode 100644
index 0000000000..2f03ff7914
--- /dev/null
+++ b/trinity-devel/patches/patch-Inchworm_Makefile
@@ -0,0 +1,15 @@
+$NetBSD$
+
+--- Inchworm/Makefile.orig	2018-09-01 15:18:14 UTC
++++ Inchworm/Makefile
+@@ -1,8 +1,8 @@
+ all:
+ 	mkdir -p build
+-	cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install
++	cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && ${MAKE} DESTDIR=../ install
+ 
+ clean:
+ 	@echo cleaning
+-	(cd build && make clean) || :
++	(cd build && ${MAKE} clean) || :
+ 	rm -rf ./build ./bin
diff --git a/trinity-devel/patches/patch-Makefile b/trinity-devel/patches/patch-Makefile
new file mode 100644
index 0000000000..28ff59ee4c
--- /dev/null
+++ b/trinity-devel/patches/patch-Makefile
@@ -0,0 +1,13 @@
+$NetBSD$
+
+--- Makefile.orig	2018-09-01 14:38:58 UTC
++++ Makefile
+@@ -17,7 +17,7 @@ else
+ endif
+ 
+ 
+-all: inchworm_target chrysalis_target trinity_essentials
++all: inchworm_target chrysalis_target trinity_essentials plugins
+ 	sh ./util/support_scripts/trinity_install_tests.sh
+ 
+ 
diff --git a/trinity-devel/patches/patch-trinity-plugins_Makefile b/trinity-devel/patches/patch-trinity-plugins_Makefile
new file mode 100644
index 0000000000..c647a83f1a
--- /dev/null
+++ b/trinity-devel/patches/patch-trinity-plugins_Makefile
@@ -0,0 +1,34 @@
+$NetBSD$
+
+--- trinity-plugins/Makefile.orig	2018-08-22 01:25:08 UTC
++++ trinity-plugins/Makefile
+@@ -9,12 +9,11 @@ TRIMMOMATIC_CODE=Trimmomatic-0.36
+ 
+ 
+ 
+-trinity_essentials: seqtk_target parafly_target trimmomatic_target
++trinity_essentials: scaffold_iworm_contigs_target seqtk_target
+ 
+ trimmomatic_target:
+ 	ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
+ 
+-
+ seqtk_target:
+ 	cd seqtk-trinity-0.0.2 && $(MAKE) CXX=$(CXX) CC=$(CC)
+ 	mv seqtk-trinity-0.0.2/seqtk-trinity ./BIN/.
+@@ -24,12 +23,14 @@ parafly_target:
+ 	cd ${PARAFLY_CODE} && sh ./configure --prefix=`pwd` CXX=$(CXX) CC=$(CC) CFLAGS="-fopenmp" CXXFLAGS="-fopenmp" && $(MAKE) install && \
+ 	cp bin/ParaFly ../BIN/
+ 
++scaffold_iworm_contigs_target:
++	cd scaffold_iworm_contigs && $(MAKE)
+ 
+ ##################################
+ ### Needed for downstream analyses
+ ##################################
+ 
+-plugins: slclust_target collectl_target
++plugins: collectl_target
+ 	@echo "\n\n** Done building plugins **\n\n"
+ 
+ 
diff --git a/trinity-devel/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile b/trinity-devel/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
new file mode 100644
index 0000000000..954a31f7a3
--- /dev/null
+++ b/trinity-devel/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
@@ -0,0 +1,15 @@
+$NetBSD$
+
+--- trinity-plugins/scaffold_iworm_contigs/Makefile.orig	2018-08-22 01:25:08 UTC
++++ trinity-plugins/scaffold_iworm_contigs/Makefile
+@@ -1,8 +1,8 @@
+-CXX    = g++
++CXX    ?= g++
+ prefix = ../htslib
+ 
+ ScaffoldIwormContigs:
+-	$(CXX) $(LDFLAGS) -I$(prefix) -L$(prefix) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs
++	$(CXX) $(LDFLAGS) -I$(LOCALBASE)/include -L$(LOCALBASE)/lib ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs
+ 
+ clean:
+ 	rm -f scaffold_iworm_contigs
diff --git a/trinity-devel/patches/patch-util_support__scripts_plugin__install__tests.sh b/trinity-devel/patches/patch-util_support__scripts_plugin__install__tests.sh
new file mode 100644
index 0000000000..5fb5e007b4
--- /dev/null
+++ b/trinity-devel/patches/patch-util_support__scripts_plugin__install__tests.sh
@@ -0,0 +1,13 @@
+$NetBSD$
+
+--- util/support_scripts/plugin_install_tests.sh.orig	2018-09-01 15:43:40 UTC
++++ util/support_scripts/plugin_install_tests.sh
+@@ -3,7 +3,7 @@
+ echo "## Checking plugin installations:"
+ echo
+ 
+-if [ -e "trinity-plugins/slclust/bin/slclust" ]
++if [ -e "${LOCALBASE}/bin/slclust" ]
+ then
+ 	echo "slclust:                 has been Installed Properly"
+ else
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