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trinity-devel: Test new version before removing old
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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