svn commit: r493402 - in head/biology/unanimity: . files

Jason W. Bacon jwb at FreeBSD.org
Wed Feb 20 01:36:54 UTC 2019 

Author: jwb
Date: Wed Feb 20 01:36:51 2019
New Revision: 493402
URL: https://svnweb.freebsd.org/changeset/ports/493402

Log:
  biology/unanimity: Upgrade to 3.4.0
  
  Switch from cmake to new meson build system
  Tests disabled for now pending work on unbundling googletest

Added:
  head/biology/unanimity/files/patch-meson.build   (contents, props changed)
  head/biology/unanimity/files/patch-meson__options.txt   (contents, props changed)
  head/biology/unanimity/files/patch-src_variantCaller_variantCaller.cpp   (contents, props changed)
  head/biology/unanimity/pkg-plist   (contents, props changed)
Deleted:
  head/biology/unanimity/files/patch-CMakeLists.txt
  head/biology/unanimity/files/patch-cmake_uny-config.cmake
  head/biology/unanimity/files/patch-cmake_uny-gitsha1.cmake
  head/biology/unanimity/files/patch-src_CMakeLists.txt
Modified:
  head/biology/unanimity/Makefile
  head/biology/unanimity/distinfo

Modified: head/biology/unanimity/Makefile
==============================================================================
--- head/biology/unanimity/Makefile	Wed Feb 20 00:50:37 2019	(r493401)
+++ head/biology/unanimity/Makefile	Wed Feb 20 01:36:51 2019	(r493402)
@@ -2,8 +2,7 @@
 
 PORTNAME=		unanimity
 DISTVERSIONPREFIX=	v
-DISTVERSION=		3.1.0
-PORTREVISION=		2
+DISTVERSION=		3.4.0
 CATEGORIES=		biology
 
 MAINTAINER=	jwb at FreeBSD.org
@@ -14,30 +13,31 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BROKEN_aarch64=		fails to compile: mmintrin.h:47:5: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
 
-# Sensitive to dependency versions, use latest commit for everything
-BUILD_DEPENDS=	pbseqan>=g20171002:biology/pbseqan \
-		pbbam>=g20180416:biology/pbbam \
-		pbcopper>=g20180413:biology/pbcopper
+# Very sensitive to pbbam and pbcopper versions!
+# Fully test new combinations and upgrade them together.
+BUILD_DEPENDS=	seqan>=2.4.0:biology/seqan \
+		swig30>=3.0:devel/swig30 \
+		${PYNUMPY}
 LIB_DEPENDS=	libhts.so:biology/htslib \
-		libboost_regex.so:devel/boost-libs
+		libboost_regex.so:devel/boost-libs \
+		libpbbam.so.0.18.0:biology/pbbam \
+		libpbcopper.so.0.4.1:biology/pbcopper
+RUN_DEPENDS=	${PYNUMPY}
 
-USES=		cmake:insource compiler:c++14-lang pkgconfig python
+# Meson needs BOOST_ROOT=${LOCALBASE}
+# https://github.com/mesonbuild/meson/issues/2239
+USES=		compiler:c++14-lang localbase meson pkgconfig python
+USE_LDCONFIG=	yes
 USE_GITHUB=	yes
 GH_ACCOUNT=	PacificBiosciences
 
-CMAKE_ARGS+=	-DHTSLIB_INCLUDE_DIRS:STRING=${LOCALBASE}/include/htslib \
-		-DHTSLIB_LIBRARIES:STRING="-L${LOCALBASE}/lib -lhts" \
-		-DPacBioBAM_INCLUDE_DIRS:STRING=${LOCALBASE}/include/pbbam \
-		-DPacBioBAM_LIBRARIES:STRING="-L${LOCALBASE}/lib -lpbbam" \
-		-DSEQAN_INCLUDE_DIRS:STRING=${LOCALBASE}/include/PacBio \
-		-Dpbcopper_INCLUDE_DIRS=${LOCALBASE}/include \
-		-Dpbcopper_LIBRARIES="-L${LOCALBASE}/lib -lpbcopper"
 CFLAGS_i386=	-msse2 -Wno-c++11-narrowing
+LDFLAGS+=	-lexecinfo
 
-PLIST_FILES=	bin/arrow bin/ccs bin/gcpp lib/libcc2.a lib/libunanimity.a
-
 post-install:
-	${INSTALL_DATA} ${WRKSRC}/src/libcc2.a ${WRKSRC}/src/libunanimity.a \
-		${STAGEDIR}${PREFIX}/lib
+	${RLN} ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0.0 \
+		${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0
+	${RLN} ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0.0 \
+		${STAGEDIR}${PREFIX}/lib/libunanimity.so.3
 
 .include <bsd.port.mk>

Modified: head/biology/unanimity/distinfo
==============================================================================
--- head/biology/unanimity/distinfo	Wed Feb 20 00:50:37 2019	(r493401)
+++ head/biology/unanimity/distinfo	Wed Feb 20 01:36:51 2019	(r493402)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1534907295
-SHA256 (PacificBiosciences-unanimity-v3.1.0_GH0.tar.gz) = 355866bd3f83bf1f7c322269c01d3c2f943e30942455741d6e802b0ad3f89912
-SIZE (PacificBiosciences-unanimity-v3.1.0_GH0.tar.gz) = 6493202
+TIMESTAMP = 1550617512
+SHA256 (PacificBiosciences-unanimity-v3.4.0_GH0.tar.gz) = cb2fd361b2cae1196e710e4d0b8af3b03a7f09145f96ce8aa7d2aef2401ca8e0
+SIZE (PacificBiosciences-unanimity-v3.4.0_GH0.tar.gz) = 6493566

Added: head/biology/unanimity/files/patch-meson.build
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/unanimity/files/patch-meson.build	Wed Feb 20 01:36:51 2019	(r493402)
@@ -0,0 +1,11 @@
+--- meson.build.orig	2019-02-17 22:59:57 UTC
++++ meson.build
+@@ -90,7 +90,7 @@ subdir('src')
+ 
+ if (not meson.is_subproject()) and get_option('swig')
+   uny_python_interp = find_program(get_option('PYTHON'), required : true)
+-  uny_swig = find_program('swig', required : true)
++  uny_swig = find_program('swig3.0', required : true)
+ 
+   uny_pv_ver = run_command(uny_python_interp, ['-c', 'import sys; sys.stdout.write(sys.version[:3])']).stdout()
+   message('Python version: ' + uny_pv_ver)

Added: head/biology/unanimity/files/patch-meson__options.txt
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/unanimity/files/patch-meson__options.txt	Wed Feb 20 01:36:51 2019	(r493402)
@@ -0,0 +1,8 @@
+--- meson_options.txt.orig	2019-02-17 22:53:47 UTC
++++ meson_options.txt
+@@ -1,4 +1,4 @@
+-option('tests',            type : 'boolean', value : true,  description : 'Enable dependencies required for testing')
++option('tests',            type : 'boolean', value : false,  description : 'Enable dependencies required for testing')
+ 
+ # python:
+ option('swig',             type : 'boolean', value : true,        description : 'Build UNANMITIY\'s SWIG interfacing code')

Added: head/biology/unanimity/files/patch-src_variantCaller_variantCaller.cpp
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/unanimity/files/patch-src_variantCaller_variantCaller.cpp	Wed Feb 20 01:36:51 2019	(r493402)
@@ -0,0 +1,9 @@
+--- src/variantCaller/variantCaller.cpp.orig	2019-02-17 23:15:10 UTC
++++ src/variantCaller/variantCaller.cpp
+@@ -1,5 +1,6 @@
+ // Author: David Seifert
+ 
++#include <iostream>
+ #include <fstream>
+ #include <string>
+ 

Added: head/biology/unanimity/pkg-plist
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/unanimity/pkg-plist	Wed Feb 20 01:36:51 2019	(r493402)
@@ -0,0 +1,82 @@
+bin/ChimeraLabeler
+bin/arrow
+bin/ccs
+bin/ccs_sim
+bin/gcpp
+bin/genomic_sim
+bin/variantCaller
+include/pacbio/UnanimityConfig.h
+include/pacbio/UnanimityVersion.h
+include/pacbio/align/AffineAlignment.h
+include/pacbio/align/AlignConfig.h
+include/pacbio/align/BandedAligner.h
+include/pacbio/align/BandedChainAlignment.h
+include/pacbio/align/ChainScorer.h
+include/pacbio/align/ChainSeeds.h
+include/pacbio/align/ChainSeedsConfig.h
+include/pacbio/align/FilterSeeds.h
+include/pacbio/align/FindSeeds.h
+include/pacbio/align/FindSeedsConfig.h
+include/pacbio/align/HomopolymerHasher.h
+include/pacbio/align/LinearAlignment.h
+include/pacbio/align/LocalAlignment.h
+include/pacbio/align/PairwiseAlignment.h
+include/pacbio/align/SeedScorer.h
+include/pacbio/align/SparseAlignment.h
+include/pacbio/align/internal/BCAlignBlocks.h
+include/pacbio/align/internal/BCAlignImpl.h
+include/pacbio/ccs/Consensus.h
+include/pacbio/ccs/ConsensusSettings.h
+include/pacbio/ccs/SparseAlignment.h
+include/pacbio/ccs/Whitelist.h
+include/pacbio/chimera/ChimeraLabel.h
+include/pacbio/chimera/ChimeraLabeler.h
+include/pacbio/chimera/ChimeraResultWriter.h
+include/pacbio/consensus/AbstractMatrix.h
+include/pacbio/consensus/Coverage.h
+include/pacbio/consensus/EasyReadScorer.h
+include/pacbio/consensus/Evaluator.h
+include/pacbio/consensus/Integrator.h
+include/pacbio/consensus/IntervalMask.h
+include/pacbio/consensus/MatrixViewConvention.h
+include/pacbio/consensus/ModelConfig.h
+include/pacbio/consensus/ModelSelection.h
+include/pacbio/consensus/Mutation.h
+include/pacbio/consensus/Polish.h
+include/pacbio/consensus/PolishResult.h
+include/pacbio/consensus/Template.h
+include/pacbio/consensus/internal/ModelInternalInitializer.h
+include/pacbio/data/ChemistryMapping.h
+include/pacbio/data/ChemistryTriple.h
+include/pacbio/data/Interval.h
+include/pacbio/data/IntervalTree.h
+include/pacbio/data/PlainOption.h
+include/pacbio/data/Read.h
+include/pacbio/data/ReadId.h
+include/pacbio/data/Sequence.h
+include/pacbio/data/State.h
+include/pacbio/data/StrandType.h
+include/pacbio/data/SubreadResultCounter.h
+include/pacbio/data/internal/BaseEncoding.h
+include/pacbio/data/internal/ConversionFunctions.h
+include/pacbio/denovo/PoaConsensus.h
+include/pacbio/denovo/PoaGraph.h
+include/pacbio/denovo/RangeFinder.h
+include/pacbio/denovo/SparsePoa.h
+include/pacbio/exception/CCSExceptions.h
+include/pacbio/exception/InvalidEvaluatorException.h
+include/pacbio/exception/ModelError.h
+include/pacbio/exception/StateError.h
+include/pacbio/io/Utility.h
+include/pacbio/parallel/WorkQueue.h
+include/pacbio/util/ExecUtils.h
+include/pacbio/util/Timer.h
+lib/libunanimity.so
+lib/libunanimity.so.3
+lib/libunanimity.so.3.0
+lib/libunanimity.so.3.0.0
+%%PYTHON_SITELIBDIR%%/ConsensusCore2.py
+%%PYTHON_SITELIBDIR%%/ConsensusCore2.pyc
+%%PYTHON_SITELIBDIR%%/ConsensusCore2.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/_ConsensusCore2.so
+libdata/pkgconfig/unanimity.pc

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