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trinity-devel: Clean up and test

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Mon Sep 17 10:39:07 2018 -0500
Changeset:	9635953c82fb42f59f35122e9c0c170d3fbf9d60

Modified Files:
	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: Clean up and test

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=9635953c82fb42f59f35122e9c0c170d3fbf9d60

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

diffstat:
 trinity-devel/Makefile                             | 36 +++++++++++++---------
 trinity-devel/PLIST                                |  1 -
 trinity-devel/distinfo                             | 16 +++++-----
 .../patches/patch-Chrysalis_CMakeLists.txt         |  1 +
 trinity-devel/patches/patch-Chrysalis_Makefile     |  1 +
 .../patches/patch-Inchworm_CMakeLists.txt          |  1 +
 trinity-devel/patches/patch-Inchworm_Makefile      |  1 +
 trinity-devel/patches/patch-Makefile               |  1 +
 .../patches/patch-trinity-plugins_Makefile         |  1 +
 ...inity-plugins_scaffold__iworm__contigs_Makefile |  1 +
 ...util_support__scripts_plugin__install__tests.sh |  1 +
 11 files changed, 38 insertions(+), 23 deletions(-)

diffs:
diff --git a/trinity-devel/Makefile b/trinity-devel/Makefile
index 43f28a25b5..e6e6df2ba4 100644
--- a/trinity-devel/Makefile
+++ b/trinity-devel/Makefile
@@ -19,7 +19,6 @@
 # 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
@@ -45,24 +44,25 @@ LICENSE=	modified-bsd
 
 USE_LANGUAGES=	c c++
 USE_JAVA=	run
-USE_TOOLS+=	cmake gmake pax perl
+USE_TOOLS+=	bash cmake gmake pax perl
 
 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=	Trinity util/*.pl util/*/*.pl util/*/*/*.pl Chrysalis/analysis/*.pl 
+REPLACE_BASH+=	util/*/*/*.sh
+REPLACE_BASH+=	Analysis/*/*/*.sh
+REPLACE_PERL=	Trinity util/misc/Monarch
+REPLACE_PERL+=	util/*.pl util/*/*.pl util/*/*/*.pl util/*/*/*/*.pl
+REPLACE_PERL+=	Chrysalis/analysis/*.pl
+REPLACE_PERL+=	Analysis/*/*.pl Analysis/*/*/*.pl Analysis/*/*/*/*.pl
+REPLACE_PERL+=	Analysis/*/*.cgi Analysis/*/PtR
+REPLACE_PERL+=	PerlLib/*.pm PerlLib/*/*.pm PerlLib/*.ph PerlLib/*.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*
+REPLACE_RSCRIPT+=	Analysis/*/*.Rscript
+REPLACE_RSCRIPT+=	util/misc/*.Rscript
 
 SUBST_CLASSES+=		paths
 SUBST_STAGE.paths=	post-patch
@@ -70,7 +70,7 @@ 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|$$ROOTDIR/trinity-plugins/Trimmomatic|${LOCALBASE}/share/Trimmomatic|g'
+SUBST_SED.paths+=	-e 's|$$ROOTDIR/trinity-plugins/Trimmomatic|${PREFIX}/share/Trimmomatic|g'
 SUBST_FILES.paths+=	${WRKSRC}/Trinity
 
 SUBST_CLASSES+=		jelly
@@ -101,19 +101,26 @@ SUBST_FILES.build+=	${WRKSRC}/trinity-plugins/COLLECTL/collectl/collectl
 SUBST_FILES.build+=	${WRKSRC}/trinity-plugins/COLLECTL/collectl/*.pl
 
 CFLAGS+=	-fopenmp
-CXXFLAGS=	-fopenmp 
-FFLAGS=		-fopenmp 
+CXXFLAGS=	-fopenmp
 
 PV=		2.8.3
 EXAMPLESDIR=	${PREFIX}/share/examples/trinity
 LIBEXEC_DIR=	${PREFIX}/libexec/trinity
 PLUGINS_DIR=	${LIBEXEC_DIR}/trinity-plugins
 
+REPLACE_INTERPRETER+=	Rscript
+REPLACE.Rscript.old=	.*Rscript
+REPLACE.Rscript.new=	${PREFIX}/bin/Rscript
+REPLACE_FILES.Rscript=	${REPLACE_RSCRIPT}
+
 # Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
 # .include "../../mk/bsd.prefs.mk"
 
 INSTALLATION_DIRS=	bin libexec/trinity/Chrysalis/bin libexec/trinity/Inchworm/bin libexec/trinity/Butterfly libexec/trinity/trinity-plugins/scaffold_iworm_contigs libexec/trinity/trinity-plugins/BIN share/examples
 
+post-extract:
+	${CHMOD} -R g-w ${WRKSRC}
+
 # FIXME: More may need to be installed
 do-install:
 	${INSTALL_SCRIPT} ${WRKSRC}/Trinity ${DESTDIR}${PREFIX}/bin
@@ -139,6 +146,7 @@ do-install:
 		${DESTDIR}${EXAMPLESDIR}
 	${LN} -fs ${PREFIX}/bin/Trinity \
 		${DESTDIR}${PREFIX}/libexec/trinity/Trinity
+	${RM} ${DESTDIR}${PREFIX}/libexec/trinity/util/support_scripts/plugin_install_tests.sh.orig
 
 .include "../../lang/python/application.mk"
 .include "../../biology/htslib/buildlink3.mk"
diff --git a/trinity-devel/PLIST b/trinity-devel/PLIST
index d3d104c695..d04d0ed9af 100644
--- a/trinity-devel/PLIST
+++ b/trinity-devel/PLIST
@@ -484,7 +484,6 @@ libexec/trinity/util/support_scripts/outfmt6_add_percent_match_length.pl
 libexec/trinity/util/support_scripts/partition_chrysalis_graphs_n_reads.pl
 libexec/trinity/util/support_scripts/partitioned_trinity_aggregator.pl
 libexec/trinity/util/support_scripts/plugin_install_tests.sh
-libexec/trinity/util/support_scripts/plugin_install_tests.sh.orig
 libexec/trinity/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl
 libexec/trinity/util/support_scripts/print_butterfly_assemblies.pl
 libexec/trinity/util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl
diff --git a/trinity-devel/distinfo b/trinity-devel/distinfo
index f2fcfd1186..1a18fb467e 100644
--- a/trinity-devel/distinfo
+++ b/trinity-devel/distinfo
@@ -4,12 +4,12 @@ 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-Chrysalis_CMakeLists.txt) = cc637a1b8dbbd95e49c94ac3c1bd361612bc01ee
+SHA1 (patch-Chrysalis_Makefile) = 151e0c2838db9822858879fa15c47a76f75f33bb
+SHA1 (patch-Inchworm_CMakeLists.txt) = 0a00585801893b2ebac759ecf5db91b76218238f
+SHA1 (patch-Inchworm_Makefile) = 43279c6a1d6c2d1a00d5f993c734122b351ff517
+SHA1 (patch-Makefile) = a428497a9d0a674d210ab5dde97d18ac9b0adba2
+SHA1 (patch-trinity-plugins_Makefile) = a7f6526429ed3007d0336fc765fd61161f9a3ed5
+SHA1 (patch-trinity-plugins_scaffold__iworm__contigs_Makefile) = 65b8d5c5bb46448080515968f6bb49df463567be
 SHA1 (patch-trinity-plugins_seqtk-trinity-0.0.2_Makefile) = 30946c32223ae06311e7315a467af5c5de626f0c
-SHA1 (patch-util_support__scripts_plugin__install__tests.sh) = 5da1d3872d6632ffb33a84f4cd4ee57c367130f3
+SHA1 (patch-util_support__scripts_plugin__install__tests.sh) = ecfe2717a827a16df01834fba8e73a8fc09ed6d7
diff --git a/trinity-devel/patches/patch-Chrysalis_CMakeLists.txt b/trinity-devel/patches/patch-Chrysalis_CMakeLists.txt
index dd6a5f0416..49a7dbae42 100644
--- a/trinity-devel/patches/patch-Chrysalis_CMakeLists.txt
+++ b/trinity-devel/patches/patch-Chrysalis_CMakeLists.txt
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Portability
 --- 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} 
diff --git a/trinity-devel/patches/patch-Chrysalis_Makefile b/trinity-devel/patches/patch-Chrysalis_Makefile
index d9e215adc7..b77ae5f267 100644
--- a/trinity-devel/patches/patch-Chrysalis_Makefile
+++ b/trinity-devel/patches/patch-Chrysalis_Makefile
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Must use gmake
 --- Chrysalis/Makefile.orig	2018-09-01 15:20:04 UTC
 +++ Chrysalis/Makefile
 @@ -1,13 +1,13 @@
diff --git a/trinity-devel/patches/patch-Inchworm_CMakeLists.txt b/trinity-devel/patches/patch-Inchworm_CMakeLists.txt
index 5136908481..784afd9776 100644
--- a/trinity-devel/patches/patch-Inchworm_CMakeLists.txt
+++ b/trinity-devel/patches/patch-Inchworm_CMakeLists.txt
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Portability
 --- 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} 
diff --git a/trinity-devel/patches/patch-Inchworm_Makefile b/trinity-devel/patches/patch-Inchworm_Makefile
index 2f03ff7914..fe44c2675f 100644
--- a/trinity-devel/patches/patch-Inchworm_Makefile
+++ b/trinity-devel/patches/patch-Inchworm_Makefile
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Must use gmake
 --- Inchworm/Makefile.orig	2018-09-01 15:18:14 UTC
 +++ Inchworm/Makefile
 @@ -1,8 +1,8 @@
diff --git a/trinity-devel/patches/patch-Makefile b/trinity-devel/patches/patch-Makefile
index 28ff59ee4c..28d726fc08 100644
--- a/trinity-devel/patches/patch-Makefile
+++ b/trinity-devel/patches/patch-Makefile
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Build plugins
 --- Makefile.orig	2018-09-01 14:38:58 UTC
 +++ Makefile
 @@ -17,7 +17,7 @@ else
diff --git a/trinity-devel/patches/patch-trinity-plugins_Makefile b/trinity-devel/patches/patch-trinity-plugins_Makefile
index c647a83f1a..95677e3641 100644
--- a/trinity-devel/patches/patch-trinity-plugins_Makefile
+++ b/trinity-devel/patches/patch-trinity-plugins_Makefile
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Unbundle deps, build scaffold_iworm_contigs
 --- trinity-plugins/Makefile.orig	2018-08-22 01:25:08 UTC
 +++ trinity-plugins/Makefile
 @@ -9,12 +9,11 @@ TRIMMOMATIC_CODE=Trimmomatic-0.36
diff --git a/trinity-devel/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile b/trinity-devel/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
index 954a31f7a3..40007968f5 100644
--- a/trinity-devel/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
+++ b/trinity-devel/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Respect pkgsrc env
 --- trinity-plugins/scaffold_iworm_contigs/Makefile.orig	2018-08-22 01:25:08 UTC
 +++ trinity-plugins/scaffold_iworm_contigs/Makefile
 @@ -1,8 +1,8 @@
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
index 5fb5e007b4..e947754ea3 100644
--- a/trinity-devel/patches/patch-util_support__scripts_plugin__install__tests.sh
+++ b/trinity-devel/patches/patch-util_support__scripts_plugin__install__tests.sh
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Unbundle slclust
 --- 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 @@
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