mirror/freebsd-ports
1
0
Fork 0
mirror of https://git.FreeBSD.org/ports.git synced 2024-12-11 02:50:24 +00:00
Code Issues Releases Activity

biology/unanimity: Upgrade to 3.4.0

Browse Source 
Switch from cmake to new meson build system
Tests disabled for now pending work on unbundling googletest
This commit is contained in:
Jason W. Bacon 2019-02-20 01:36:51 +00:00
parent a90b307d81
commit 1895acd462
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=493402
10 changed files with 132 additions and 69 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

38
biology/unanimity/Makefile
View File

@ -2,8 +2,7 @@
PORTNAME= unanimity
DISTVERSIONPREFIX= v
DISTVERSION= 3.1.0
PORTREVISION= 2
DISTVERSION= 3.4.0
CATEGORIES= biology
MAINTAINER= jwb@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
PLIST_FILES= bin/arrow bin/ccs bin/gcpp lib/libcc2.a lib/libunanimity.a
LDFLAGS+= -lexecinfo
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>

6
biology/unanimity/distinfo
View File

@ -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

11
biology/unanimity/files/patch-CMakeLists.txt
View File

@ -1,11 +0,0 @@
--- CMakeLists.txt.orig 2018-03-07 23:10:34 UTC
+++ CMakeLists.txt
@@ -37,7 +37,7 @@ include(uny-ccache)
include(uny-releasewithassert)
include(uny-dependencies)
include(uny-compilerflags)
-include(uny-gitsha1)
+# include(uny-gitsha1)
include(uny-config)
# Build library

10
biology/unanimity/files/patch-cmake_uny-config.cmake
View File

@ -1,10 +0,0 @@
--- cmake/uny-config.cmake.orig 2016-09-12 19:55:43 UTC
+++ cmake/uny-config.cmake
@@ -1,6 +1,6 @@
# Config generation
-find_git_sha1(UNANIMITY_GIT_SHA1)
+# find_git_sha1(UNANIMITY_GIT_SHA1)
file (STRINGS "${UNY_RootDir}/CHANGELOG.md" UNANIMITY_CHANGELOG)

11
biology/unanimity/files/patch-cmake_uny-gitsha1.cmake
View File

@ -1,11 +0,0 @@
--- cmake/uny-gitsha1.cmake.orig 2018-03-07 23:10:34 UTC
+++ cmake/uny-gitsha1.cmake
@@ -7,7 +7,7 @@ set(__find_git_sha1 YES)
function(find_git_sha1 _GIT_SHA1)
find_package(Git QUIET REQUIRED)
execute_process(COMMAND
- "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=-dirty"
+ echo 6f11a13e1472b8c00337ba8c5e94bf83bdab31d6
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
RESULT_VARIABLE res
OUTPUT_VARIABLE out

11
biology/unanimity/files/patch-meson.build Normal file
View File

@ -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)

8
biology/unanimity/files/patch-meson__options.txt Normal file
View File

@ -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')

15
biology/unanimity/files/patch-src_CMakeLists.txt
View File

@ -1,15 +0,0 @@
--- src/CMakeLists.txt.orig 2018-03-07 23:10:34 UTC
+++ src/CMakeLists.txt
@@ -53,11 +53,11 @@ configure_file(
# includes
set(UNY_INCLUDE_DIRS
+ ${SEQAN_INCLUDE_DIRS}
${UNY_IncludeDir}
${CMAKE_BINARY_DIR}/generated
${Boost_INCLUDE_DIRS}
${HTSLIB_INCLUDE_DIRS}
- ${SEQAN_INCLUDE_DIRS}
${CPPOPTPARSE_IncludeDir}
${PacBioBAM_INCLUDE_DIRS}
${pbcopper_INCLUDE_DIRS}

9
biology/unanimity/files/patch-src_variantCaller_variantCaller.cpp Normal file
View File

@ -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>

82
biology/unanimity/pkg-plist Normal file
View File

@ -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