diff options
Diffstat (limited to 'biology/metaeuk')
| -rw-r--r-- | biology/metaeuk/Makefile | 46 | ||||
| -rw-r--r-- | biology/metaeuk/distinfo | 7 | ||||
| -rw-r--r-- | biology/metaeuk/pkg-descr | 8 |
3 files changed, 61 insertions, 0 deletions
diff --git a/biology/metaeuk/Makefile b/biology/metaeuk/Makefile new file mode 100644 index 000000000000..0281783cad7a --- /dev/null +++ b/biology/metaeuk/Makefile @@ -0,0 +1,46 @@ +PORTNAME= metaeuk +DISTVERSION= 7 +DISTVERSIONSUFFIX= -bba0d80 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Gene discovery and annotation for large-scale eukaryotic metagenomics +WWW= https://github.com/soedinglab/metaeuk + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENCE.md + +NOT_FOR_ARCHS= armv6 armv7 i386 mips powerpc # 32-bit platforms produce wrong results based on https://github.com/soedinglab/metaeuk/issues/85#issuecomment-1888379107 +NOT_FOR_ARCHS+= powerpc64 # many modules produce wrong results on big-endian architectures +BROKEN_powerpc64le= clang crashes, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=276268 + +BUILD_DEPENDS= xxd:editors/vim +TEST_DEPENDS= bash:shells/bash + +USES= cmake perl5 shebangfix +USE_PERL5= build + +USE_GITHUB= yes +GH_ACCOUNT= soedinglab +GH_TUPLE= soedinglab:metaeuk-regression:f7c3999:metaeuk_regression/tests \ + soedinglab:MMseqs2-Regression:5e3bc17:MMseqs2_Regression/lib/mmseqs/util/regression + +SHEBANG_GLOB= *.sh + +PLIST_FILES= bin/metaeuk + +CMAKE_OFF= NATIVE_ARCH + +.include <bsd.port.options.mk> + +.if !exists(/usr/include/omp.h) || ${ARCH} == powerpc64le # https://github.com/soedinglab/metaeuk/issues/85, https://github.com/llvm/llvm-project/issues/63807 +CMAKE_ARGS+= -DREQUIRE_OPENMP:BOOL=OFF + +post-patch: # workaround for https://github.com/soedinglab/metaeuk/issues/55 + @${REINPLACE_CMD} -e 's|set(REQUIRE_OPENMP 1 |set(REQUIRE_OPENMP 0 |' ${WRKSRC}/lib/mmseqs/src/CMakeLists.txt +.endif + +do-test: + @cd ${WRKSRC}/tests && ./run.sh ${STAGEDIR}${PREFIX}/bin/metaeuk + +.include <bsd.port.mk> diff --git a/biology/metaeuk/distinfo b/biology/metaeuk/distinfo new file mode 100644 index 000000000000..3aa2029fb5e3 --- /dev/null +++ b/biology/metaeuk/distinfo @@ -0,0 +1,7 @@ +TIMESTAMP = 1717132294 +SHA256 (soedinglab-metaeuk-7-bba0d80_GH0.tar.gz) = 45eff3cb8e15626b1142d4717bf43a6e7a1308bc8a6eb1718c70d33d613898fa +SIZE (soedinglab-metaeuk-7-bba0d80_GH0.tar.gz) = 13342465 +SHA256 (soedinglab-metaeuk-regression-f7c3999_GH0.tar.gz) = 4724516451e7d9d977c4d2edc04ab86188d5e0326f00fbc6e208df241ac0b1b3 +SIZE (soedinglab-metaeuk-regression-f7c3999_GH0.tar.gz) = 6720389 +SHA256 (soedinglab-MMseqs2-Regression-5e3bc17_GH0.tar.gz) = 415a7e81821c5add73c8c3b450acbd316d7244d151a306864ff3c260b115b7be +SIZE (soedinglab-MMseqs2-Regression-5e3bc17_GH0.tar.gz) = 27715323 diff --git a/biology/metaeuk/pkg-descr b/biology/metaeuk/pkg-descr new file mode 100644 index 000000000000..2ab6502d6c02 --- /dev/null +++ b/biology/metaeuk/pkg-descr @@ -0,0 +1,8 @@ +MetaEuk is a modular toolkit designed for large-scale gene discovery and +annotation in eukaryotic metagenomic contigs. MetaEuk combines the fast and +sensitive homology search capabilities of MMseqs2 with a dynamic programming +procedure to recover optimal exons sets. It reduces redundancies in multiple +discoveries of the same gene and resolves conflicting gene predictions on the +same strand. MetaEuk is GPLv3-licensed open source software that is implemented +in C++ and available for Linux and macOS. The software is designed to run +efficiently on multiple cores. |