diff options
Diffstat (limited to 'biology')
108 files changed, 401 insertions, 580 deletions
diff --git a/biology/Makefile b/biology/Makefile index ea85f35b064d..d4ba88800bfe 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -37,7 +37,6 @@ SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta - SUBDIR += checkm SUBDIR += chip-seq SUBDIR += clustal-omega SUBDIR += clustalw @@ -190,11 +189,10 @@ SUBDIR += py-multiqc SUBDIR += py-newick SUBDIR += py-ont-fast5-api - SUBDIR += py-orange3-bioinformatics - SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-py2bit SUBDIR += py-pybigwig + SUBDIR += py-pydeseq2 SUBDIR += py-pyfaidx SUBDIR += py-pyrodigal SUBDIR += py-pysam diff --git a/biology/augustus/Makefile b/biology/augustus/Makefile index d22379a4bdb8..147d25ad6850 100644 --- a/biology/augustus/Makefile +++ b/biology/augustus/Makefile @@ -1,7 +1,7 @@ PORTNAME= augustus DISTVERSIONPREFIX= v DISTVERSION= 3.5.0 -PORTREVISION= 13 +PORTREVISION= 14 CATEGORIES= biology science PKGNAMESUFFIX= -gene-prediction diff --git a/biology/bamtools/Makefile b/biology/bamtools/Makefile index 8ba4a4d667ec..775c1f88cb59 100644 --- a/biology/bamtools/Makefile +++ b/biology/bamtools/Makefile @@ -1,7 +1,6 @@ PORTNAME= bamtools DISTVERSIONPREFIX= v -DISTVERSION= 2.5.2 -PORTREVISION= 2 +DISTVERSION= 2.5.3 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -19,4 +18,6 @@ GH_ACCOUNT= pezmaster31 CMAKE_ON+= BUILD_SHARED_LIBS +PLIST_SUB= PORTVERSION=${PORTVERSION} + .include <bsd.port.mk> diff --git a/biology/bamtools/distinfo b/biology/bamtools/distinfo index e36197452212..dd64a579b51b 100644 --- a/biology/bamtools/distinfo +++ b/biology/bamtools/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1625529459 -SHA256 (pezmaster31-bamtools-v2.5.2_GH0.tar.gz) = 4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8 -SIZE (pezmaster31-bamtools-v2.5.2_GH0.tar.gz) = 245729 +TIMESTAMP = 1747676701 +SHA256 (pezmaster31-bamtools-v2.5.3_GH0.tar.gz) = 7d4e59bac7c03bde488fe43e533692f78b5325a097328785ec31373ffac08344 +SIZE (pezmaster31-bamtools-v2.5.3_GH0.tar.gz) = 245648 diff --git a/biology/bamtools/pkg-descr b/biology/bamtools/pkg-descr index 632f635d85bd..e5116b7fbba8 100644 --- a/biology/bamtools/pkg-descr +++ b/biology/bamtools/pkg-descr @@ -1,6 +1,5 @@ BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. - BAM is the binary alternative to the sequence alignment/map (SAM) format used for storing genetic sequence data. It uses BGZF block compression implemented on top of the standard gzip file format to provide good compression while diff --git a/biology/bamtools/pkg-plist b/biology/bamtools/pkg-plist index a976799fd806..df5a98027cbe 100644 --- a/biology/bamtools/pkg-plist +++ b/biology/bamtools/pkg-plist @@ -21,5 +21,5 @@ include/bamtools/api/api_global.h include/bamtools/api/bamtools_api_export.h include/bamtools/shared/bamtools_global.h lib/libbamtools.so -lib/libbamtools.so.2.5.2 +lib/libbamtools.so.%%PORTVERSION%% libdata/pkgconfig/bamtools-1.pc diff --git a/biology/bcf-score/Makefile b/biology/bcf-score/Makefile index 0436c4b14f2d..bd2d2610e27e 100644 --- a/biology/bcf-score/Makefile +++ b/biology/bcf-score/Makefile @@ -1,6 +1,6 @@ PORTNAME= bcf-score DISTVERSION= 1.20 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= https://software.broadinstitute.org/software/score/ # Get this right, or ports will download bcftools in it's place via tuple @@ -12,7 +12,7 @@ WWW= https://software.broadinstitute.org/software/score/ LICENSE= MIT -BUILD_DEPENDS= htslib>=1.21:biology/htslib +BUILD_DEPENDS= htslib>=1.22:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib libcholmod.so:math/suitesparse-cholmod TEST_DEPENDS= bash:shells/bash RUN_DEPENDS= bash:shells/bash bcftools>=${PORTVERSION}:biology/bcftools @@ -23,7 +23,7 @@ USE_PERL5= test GH_ACCOUNT= samtools GH_PROJECT= bcftools -GH_TAGNAME= 1.21 +GH_TAGNAME= 1.22 GNU_CONFIGURE= yes SHEBANG_FILES= misc/* test/test.pl diff --git a/biology/bcf-score/distinfo b/biology/bcf-score/distinfo index fb0644c4567b..724198c182f2 100644 --- a/biology/bcf-score/distinfo +++ b/biology/bcf-score/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1727475307 +TIMESTAMP = 1750428714 SHA256 (score_1.20-20240505.tar.gz) = c2ac510f0a48e3d2e61d1a9e219e030b1268cdcf3bf987217bbd16740d962d41 SIZE (score_1.20-20240505.tar.gz) = 96852 -SHA256 (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d -SIZE (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 3665160 +SHA256 (samtools-bcftools-1.20-1.22_GH0.tar.gz) = 1608e547daf7bd5ab7d52dea57019f57da3fdfb29bc26dece1e8d01a999a9a2d +SIZE (samtools-bcftools-1.20-1.22_GH0.tar.gz) = 3751342 diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile index f04c0777bc27..3a1c7bc91002 100644 --- a/biology/bcftools/Makefile +++ b/biology/bcftools/Makefile @@ -1,5 +1,5 @@ PORTNAME= bcftools -PORTVERSION= 1.21 +PORTVERSION= 1.22 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -9,7 +9,7 @@ WWW= https://www.htslib.org/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE -BUILD_DEPENDS= htslib>=1.21:biology/htslib +BUILD_DEPENDS= htslib>=1.22:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib TEST_DEPENDS= bash:shells/bash RUN_DEPENDS= bash:shells/bash diff --git a/biology/bcftools/distinfo b/biology/bcftools/distinfo index a39dbc0e3ca0..187e684df6f4 100644 --- a/biology/bcftools/distinfo +++ b/biology/bcftools/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1727437561 -SHA256 (samtools-bcftools-1.21_GH0.tar.gz) = 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d -SIZE (samtools-bcftools-1.21_GH0.tar.gz) = 3665160 +TIMESTAMP = 1748951423 +SHA256 (samtools-bcftools-1.22_GH0.tar.gz) = 1608e547daf7bd5ab7d52dea57019f57da3fdfb29bc26dece1e8d01a999a9a2d +SIZE (samtools-bcftools-1.22_GH0.tar.gz) = 3751342 diff --git a/biology/bcftools/pkg-plist b/biology/bcftools/pkg-plist index 6aa7a6d9f73e..8d7cedf90291 100644 --- a/biology/bcftools/pkg-plist +++ b/biology/bcftools/pkg-plist @@ -45,4 +45,6 @@ libexec/bcftools/trio-stats.so libexec/bcftools/trio-switch-rate.so libexec/bcftools/variant-distance.so libexec/bcftools/variantkey-hex.so +libexec/bcftools/vcf2table.so +libexec/bcftools/vrfs.so share/man/man1/bcftools.1.gz diff --git a/biology/bifrost/Makefile b/biology/bifrost/Makefile index 8820ddfa0631..e1873b430549 100644 --- a/biology/bifrost/Makefile +++ b/biology/bifrost/Makefile @@ -1,6 +1,7 @@ PORTNAME= bifrost DISTVERSIONPREFIX= v DISTVERSION= 1.3.5 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -18,6 +19,8 @@ USE_GITHUB= yes CMAKE_ARGS= -DCOMPILATION_ARCH=${CPUTYPE:UOFF} +CXXFLAGS+= -Wno-unqualified-std-cast-call + GH_ACCOUNT= pmelsted .include <bsd.port.mk> diff --git a/biology/bifrost/distinfo b/biology/bifrost/distinfo index 49f7e2d919bb..43195678b9c9 100644 --- a/biology/bifrost/distinfo +++ b/biology/bifrost/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1710590640 +TIMESTAMP = 1748282354 SHA256 (pmelsted-bifrost-v1.3.5_GH0.tar.gz) = e1b2491328b0cc1a32e433a8a9780f05547fa4b8d674b58abdda9ac8809f5341 SIZE (pmelsted-bifrost-v1.3.5_GH0.tar.gz) = 356701 diff --git a/biology/bifrost/files/patch-CMakeLists.txt b/biology/bifrost/files/patch-CMakeLists.txt index 27893b9ec44d..4d49c5a270cc 100644 --- a/biology/bifrost/files/patch-CMakeLists.txt +++ b/biology/bifrost/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2023-08-12 14:26:29 UTC +--- CMakeLists.txt.orig 2024-03-15 15:20:17 UTC +++ CMakeLists.txt -@@ -46,7 +46,6 @@ else(CMAKE_BUILD_TYPE MATCHES Debug) +@@ -56,7 +56,6 @@ else(CMAKE_BUILD_TYPE MATCHES Debug) set(CMAKE_EXE_LINKER_FLAGS "-pg") else(CMAKE_BUILD_TYPE MATCHES Profile) message("Build type: Release") diff --git a/biology/bifrost/files/patch-src_DataStorage.tcc b/biology/bifrost/files/patch-src_DataStorage.tcc new file mode 100644 index 000000000000..22196bb8e11c --- /dev/null +++ b/biology/bifrost/files/patch-src_DataStorage.tcc @@ -0,0 +1,14 @@ +--- src/DataStorage.tcc.orig 2024-03-15 15:20:17 UTC ++++ src/DataStorage.tcc +@@ -78,7 +78,10 @@ DataStorage<U>::DataStorage(const DataStorage& o) : co + + unitig_cs_link = new atomic<uint64_t>[sz_link]; + +- for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load(); ++ // Hayzam Sherif: o.sz_link -> o.unitig_cs_link ++ // Independently proposed by Lucas van Dijk: ++ // https://github.com/pmelsted/bifrost/pull/18/files ++ for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.unitig_cs_link[i].load(); + } + + if ((o.data != nullptr) && (o.sz_cs != 0)){ diff --git a/biology/bio-mocha/Makefile b/biology/bio-mocha/Makefile index a9228be3a30e..828b246380b0 100644 --- a/biology/bio-mocha/Makefile +++ b/biology/bio-mocha/Makefile @@ -1,5 +1,6 @@ PORTNAME= bio-mocha DISTVERSION= 1.20 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= https://software.broadinstitute.org/software/mocha/ # Get this right, or ports will download bcftools in it's place via tuple @@ -11,7 +12,7 @@ WWW= https://software.broadinstitute.org/software/mocha/ LICENSE= MIT -BUILD_DEPENDS= bash:shells/bash htslib>=1.21:biology/htslib +BUILD_DEPENDS= bash:shells/bash htslib>=1.22:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib RUN_DEPENDS= bcftools>=${PORTVERSION}:biology/bcftools @@ -21,7 +22,7 @@ USE_PERL5= test GH_ACCOUNT= samtools GH_PROJECT= bcftools -GH_TAGNAME= 1.21 +GH_TAGNAME= 1.22 GNU_CONFIGURE= yes SHEBANG_FILES= misc/* test/test.pl diff --git a/biology/bio-mocha/distinfo b/biology/bio-mocha/distinfo index 6f2f8b800396..6485cffc5d72 100644 --- a/biology/bio-mocha/distinfo +++ b/biology/bio-mocha/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1727475837 +TIMESTAMP = 1750428898 SHA256 (bio-mocha_1.20-20240505.tar.gz) = 3beeb7f046b491fed162dfedd83a29b3eebb165fb1f2a25f44df7fa2f063793b SIZE (bio-mocha_1.20-20240505.tar.gz) = 66752 -SHA256 (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d -SIZE (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 3665160 +SHA256 (samtools-bcftools-1.20-1.22_GH0.tar.gz) = 1608e547daf7bd5ab7d52dea57019f57da3fdfb29bc26dece1e8d01a999a9a2d +SIZE (samtools-bcftools-1.20-1.22_GH0.tar.gz) = 3751342 diff --git a/biology/biococoa/Makefile b/biology/biococoa/Makefile index 7177814e19bf..56145db6d6be 100644 --- a/biology/biococoa/Makefile +++ b/biology/biococoa/Makefile @@ -4,7 +4,6 @@ PORTREVISION= 8 CATEGORIES= biology gnustep MASTER_SITES= http://bioinformatics.org/biococoa/downloads/ DISTNAME= biococoa-${PORTVERSION}-src -EXTRACT_SUFX= .tgz MAINTAINER= ports@FreeBSD.org COMMENT= Bioinformatics framework @@ -12,7 +11,7 @@ WWW= http://bioinformatics.org/biococoa/ LICENSE= LGPL21 -USES= gnustep +USES= gnustep tar:tgz USE_GNUSTEP= back build WRKSRC= ${WRKDIR}/biococoa-${PORTVERSION} diff --git a/biology/bolt-lmm/Makefile b/biology/bolt-lmm/Makefile index 4d79a94304e3..242d706fd046 100644 --- a/biology/bolt-lmm/Makefile +++ b/biology/bolt-lmm/Makefile @@ -1,6 +1,6 @@ PORTNAME= bolt-lmm DISTVERSION= 2.3.6 -PORTREVISION= 15 +PORTREVISION= 16 CATEGORIES= biology MASTER_SITES= https://data.broadinstitute.org/alkesgroup/BOLT-LMM/downloads/ DISTNAME= BOLT-LMM_v${PORTVERSION} diff --git a/biology/canu/Makefile b/biology/canu/Makefile index 5e89db673d70..8719b5143a72 100644 --- a/biology/canu/Makefile +++ b/biology/canu/Makefile @@ -1,6 +1,6 @@ PORTNAME= canu DISTVERSION= 2.2 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= biology java perl5 # Github auto-generated tarballs lack submodules MASTER_SITES= https://github.com/marbl/canu/releases/download/v${DISTVERSION}/ diff --git a/biology/checkm/Makefile b/biology/checkm/Makefile deleted file mode 100644 index cb7cc7108d4a..000000000000 --- a/biology/checkm/Makefile +++ /dev/null @@ -1,30 +0,0 @@ -PORTNAME= CheckM -DISTVERSIONPREFIX= v -DISTVERSION= 1.2.3 -PORTREVISION= 1 -CATEGORIES= biology python - -MAINTAINER= yuri@FreeBSD.org -COMMENT= Quality assessment tool for the microbial genomes -WWW= https://ecogenomics.github.io/CheckM/ - -LICENSE= GPLv3 -LICENSE_FILE= ${WRKSRC}/LICENSE - -DEPRECATED= Depends on expired science/py-DendroPy -EXPIRATION_DATE=2025-06-01 - -RUN_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}DendroPy>0:science/py-DendroPy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} - -USES= dos2unix python -USE_GITHUB= yes -GH_ACCOUNT= Ecogenomics -USE_PYTHON= distutils noflavors autoplist - -NO_ARCH= yes - -.include <bsd.port.mk> diff --git a/biology/checkm/distinfo b/biology/checkm/distinfo deleted file mode 100644 index c1da8633ab00..000000000000 --- a/biology/checkm/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1730733018 -SHA256 (Ecogenomics-CheckM-v1.2.3_GH0.tar.gz) = 5f8340e71d3256ba8cf407d27bdc7914d1aa86b14b2d63d1e32cceb325e5aa82 -SIZE (Ecogenomics-CheckM-v1.2.3_GH0.tar.gz) = 1017616 diff --git a/biology/checkm/pkg-descr b/biology/checkm/pkg-descr deleted file mode 100644 index 4238256d225a..000000000000 --- a/biology/checkm/pkg-descr +++ /dev/null @@ -1,13 +0,0 @@ -CheckM provides a set of tools for assessing the quality of genomes recovered -from isolates, single cells, or metagenomes. - -It provides robust estimates of genome completeness and contamination by using -collocated sets of genes that are ubiquitous and single-copy within a -phylogenetic lineage. - -Assessment of genome quality can also be examined using plots depicting key -genomic characteristics (e.g., GC, coding density) which highlight sequences -outside the expected distributions of a typical genome. CheckM also provides -tools for identifying genome bins that are likely candidates for merging based -on marker set compatibility, similarity in genomic characteristics, and -proximity within a reference genome tree. diff --git a/biology/coverm/Makefile b/biology/coverm/Makefile index 469eeefaa615..ed1fc1dc5fb6 100644 --- a/biology/coverm/Makefile +++ b/biology/coverm/Makefile @@ -1,7 +1,7 @@ PORTNAME= coverm DISTVERSIONPREFIX= v DISTVERSION= 0.7.0 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/cufflinks/Makefile b/biology/cufflinks/Makefile index c6be37b46701..a9029cdfe03f 100644 --- a/biology/cufflinks/Makefile +++ b/biology/cufflinks/Makefile @@ -1,7 +1,7 @@ PORTNAME= cufflinks DISTVERSIONPREFIX= v DISTVERSION= 2.2.1-89 -PORTREVISION= 11 +PORTREVISION= 12 DISTVERSIONSUFFIX= -gdc3b0cb CATEGORIES= biology diff --git a/biology/dsr-pdb/Makefile b/biology/dsr-pdb/Makefile index 16dc1bfda7e4..07f45bd9718d 100644 --- a/biology/dsr-pdb/Makefile +++ b/biology/dsr-pdb/Makefile @@ -1,6 +1,6 @@ PORTNAME= dsr-pdb DISTVERSION= 1.0.3 -PORTREVISION= 15 +PORTREVISION= 16 CATEGORIES= biology MASTER_SITES= https://graphics.stanford.edu/~drussel/ DISTNAME= ${PORTNAME} diff --git a/biology/fasda/Makefile b/biology/fasda/Makefile index 90af1fc205cb..2d85a23af573 100644 --- a/biology/fasda/Makefile +++ b/biology/fasda/Makefile @@ -1,5 +1,6 @@ PORTNAME= fasda -DISTVERSION= 0.2.0 +DISTVERSION= 0.2.0-1 +DISTVERSIONSUFFIX= -ga7d14ad CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/fasda/distinfo b/biology/fasda/distinfo index f7174b017086..ad561981d758 100644 --- a/biology/fasda/distinfo +++ b/biology/fasda/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1745682225 -SHA256 (auerlab-fasda-0.2.0_GH0.tar.gz) = 5e52e9773d70b4ffa303b91a3e156cfc706e738b3fc17503d20bfbbaefd82446 -SIZE (auerlab-fasda-0.2.0_GH0.tar.gz) = 1869574 +TIMESTAMP = 1748181140 +SHA256 (auerlab-fasda-0.2.0-1-ga7d14ad_GH0.tar.gz) = fbc12198337617a2f09a95fda627861e8ed7fa2f345ccee218879b5c58cabea7 +SIZE (auerlab-fasda-0.2.0-1-ga7d14ad_GH0.tar.gz) = 1869807 diff --git a/biology/fastp/Makefile b/biology/fastp/Makefile index 7af865fb935a..7d91034eb87c 100644 --- a/biology/fastp/Makefile +++ b/biology/fastp/Makefile @@ -1,9 +1,9 @@ PORTNAME= fastp DISTVERSIONPREFIX= v -DISTVERSION= 0.24.1 +DISTVERSION= 0.26.0 CATEGORIES= biology -MAINTAINER= jwb@FreeBSD.org +MAINTAINER= hayzam@alchemilla.io COMMENT= Ultra-fast all-in-one FASTQ preprocessor WWW= https://github.com/OpenGene/fastp diff --git a/biology/fastp/distinfo b/biology/fastp/distinfo index d33c3c0986a6..6abdf5196be5 100644 --- a/biology/fastp/distinfo +++ b/biology/fastp/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1744893121 -SHA256 (OpenGene-fastp-v0.24.1_GH0.tar.gz) = dd8a1b7e0410a800f80939e4d14b116e90bbec83ef7294a5f13fdaaba3fcc719 -SIZE (OpenGene-fastp-v0.24.1_GH0.tar.gz) = 164307 +TIMESTAMP = 1749236354 +SHA256 (OpenGene-fastp-v0.26.0_GH0.tar.gz) = ab5396f448bece92e599e4d3acc48751fc46f0f43333ca271d229aa95dc47c4e +SIZE (OpenGene-fastp-v0.26.0_GH0.tar.gz) = 166500 diff --git a/biology/fastp/files/patch-Makefile b/biology/fastp/files/patch-Makefile index 5e68e39804a1..09efd133c6d8 100644 --- a/biology/fastp/files/patch-Makefile +++ b/biology/fastp/files/patch-Makefile @@ -1,4 +1,4 @@ ---- Makefile.orig 2025-04-16 10:13:35 UTC +--- Makefile.orig 2025-06-06 00:03:48 UTC +++ Makefile @@ -7,6 +7,8 @@ LIBRARY_DIRS ?= INCLUDE_DIRS ?= @@ -9,14 +9,15 @@ SRC := $(wildcard ${DIR_SRC}/*.cpp) OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC})) -@@ -15,15 +17,20 @@ CXX ?= g++ +@@ -15,15 +17,21 @@ CXX ?= g++ BIN_TARGET := ${TARGET} CXX ?= g++ -CXXFLAGS := -std=c++11 -pthread -g -O3 -MD -MP -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS} +# Optional flags that the user can override by setting CXXFLAGS in the -+# env or make argument -+CXXFLAGS ?= -g -O3 ++# env or make argument. -pthread is a link flag, and serves no purpose ++# in the compile command. It is handled by -lpthread in LIBS. ++CXXFLAGS ?= -g -O3 -MD -MP +# Required flags +CXXFLAGS += -std=c++11 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) LIBS := -lisal -ldeflate -lpthread @@ -33,11 +34,13 @@ static:${OBJ} $(CXX) $(OBJ) -o ${BIN_TARGET} $(STATIC_LD_FLAGS) -@@ -38,8 +45,13 @@ clean: +@@ -38,8 +46,15 @@ clean: @rm -rf $(DIR_OBJ) @rm -f $(TARGET) -+# Respect DESTDIR for staged installs (used by most package managers) ++# Respect DESTDIR for staged installs (used by most package managers). ++# DESTDIR is empty by default, so this will install directly to BINDIR ++# unless DESTDIR is supplied by the user. install: - install $(TARGET) $(BINDIR)/$(TARGET) + install $(TARGET) $(DESTDIR)$(BINDIR)/$(TARGET) diff --git a/biology/haplohseq/Makefile b/biology/haplohseq/Makefile index 8da67ec49753..31e85343fe05 100644 --- a/biology/haplohseq/Makefile +++ b/biology/haplohseq/Makefile @@ -1,16 +1,16 @@ PORTNAME= haplohseq -DISTVERSION= 0.1.2 -PORTREVISION= 13 +DISTVERSION= 0.1.2-3 +PORTREVISION= 1 +DISTVERSIONSUFFIX= -gfeb9267 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Identify regions of allelic imbalance -WWW= https://sites.google.com/site/integrativecancergenomics/software/haplohseq +WWW= https://github.com/outpaddling/haplohseq \ + https://sites.google.com/site/integrativecancergenomics/software/haplohseq LICENSE= MIT -BROKEN= fails to build with Boost>=1.87 - LIB_DEPENDS= libboost_system.so:devel/boost-libs RUN_DEPENDS= R-cran-optparse>0:devel/R-cran-optparse diff --git a/biology/haplohseq/distinfo b/biology/haplohseq/distinfo index 7af7556d5596..ab9872a8d79f 100644 --- a/biology/haplohseq/distinfo +++ b/biology/haplohseq/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1611421648 -SHA256 (outpaddling-haplohseq-0.1.2_GH0.tar.gz) = 64f61023a6795decb680c23d142b1a349988d4c0e3bef8c7d52ca33bf42f29f0 -SIZE (outpaddling-haplohseq-0.1.2_GH0.tar.gz) = 12084603 +TIMESTAMP = 1747762325 +SHA256 (outpaddling-haplohseq-0.1.2-3-gfeb9267_GH0.tar.gz) = a23691f16f1c03e0dfd833896068e05eaa139d488a7094a49033aeacba948cb1 +SIZE (outpaddling-haplohseq-0.1.2-3-gfeb9267_GH0.tar.gz) = 12085111 diff --git a/biology/haplohseq/files/patch-makefile b/biology/haplohseq/files/patch-makefile deleted file mode 100644 index 5387716aa503..000000000000 --- a/biology/haplohseq/files/patch-makefile +++ /dev/null @@ -1,105 +0,0 @@ ---- makefile.orig 2019-08-29 18:03:23 UTC -+++ makefile -@@ -7,23 +7,32 @@ - # - - # Constants --CXX=g++ -+# Default to g++ if not set by make args or environment -+CXX?=g++ - #-O0 -g will turn on debugging - #The rule of thumb: - #When you need to debug, use -O0 (and -g to generate debugging symbols.) - #When you are preparing to ship it, use -O2. - #When you use gentoo, use -O3...! - #When you need to put it on an embedded system, use -Os (optimize for size, not for efficiency.) --CXX_FLAGS=-Wall -g -stdlib=libstdc++ -+# Use canonincal compiler variables, which may be provided by build env -+CXXFLAGS?=-Wall -g -stdlib=libstdc++ - SRC=src - CONF=conf - HMM_SRC=$(SRC)/hmm - UTIL_SRC=$(SRC)/util --BOOST=/usr/local/boost_1_52_0 -+BOOST?=/usr/local/boost_1_52_0 - INCLUDES=-I./$(SRC) -I./$(HMM_SRC) -I./$(UTIL_SRC) -isystem$(BOOST) --LIBRARY_PATHS=-Llib/macosx -+LIBRARY_PATHS?=-Llib/macosx - LIBRARIES=-lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread - -+# Installation target with destdir support -+DESTDIR?=. -+PREFIX?=/usr/local -+MKDIR?=mkdir -+INSTALL?=install -+STRIP?= # empty, set to -s to install stripped binary -+ - # Generated directories which are generated in this script and cleaned up with 'make clean' - BUILD=build - OBJ=$(BUILD)/obj -@@ -35,18 +44,21 @@ directories: - - # Create object files into the OBJ directory from cpp files in the SRC directory. - $(OBJ)/%.o: $(SRC)/%.cpp directories -- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $< -+ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $< - $(OBJ)/%.o: $(HMM_SRC)/%.cpp directories -- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $< -+ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $< - $(OBJ)/%.o: $(UTIL_SRC)/%.cpp directories -- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $< -+ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $< - --all: clean haplohseq -+all: haplohseq test - - haplohseq: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o -- $(CXX) -o $(BIN)/$@ $(CXX_FLAGS) $(INCLUDES) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o $(LIBRARY_PATHS) $(LIBRARIES) -- cp -r $(CONF) $(BIN)/. -- -+ $(CXX) -o $(BIN)/$@ $(CXXFLAGS) $(INCLUDES) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) -+ -+install: -+ $(MKDIR) -p $(DESTDIR)$(PREFIX)/bin -+ $(INSTALL) -c $(STRIP) $(BIN)/* $(DESTDIR)$(PREFIX)/bin -+ - clean: - rm -rf $(BUILD) - -@@ -74,28 +86,28 @@ test: FreqPhaseTest HaplohSeqTest HmmTest InputProcess - - # Create test object files into the OBJ directory from cpp files in the SRC directory. - $(TEST_BIN)/%.o: $(TEST_SRC)/%.cpp directories test_directory -- $(CXX) $(CXX_FLAGS) $(INCLUDES) $(TEST_INCLUDES) -c -o $@ $< -+ $(CXX) $(CXXFLAGS) $(INCLUDES) $(TEST_INCLUDES) -c -o $@ $< - - HaplohSeqTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - - FreqPhaseTest: $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - - HmmTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - - InputProcessorTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - - MathUtilTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - - ReporterTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - - ThreadPoolTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o -- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o $(LIBRARY_PATHS) $(LIBRARIES) -+ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS) - ############################## END TEST LOGIC ############################## - - diff --git a/biology/haplohseq/files/patch-scripts_ldmap.py b/biology/haplohseq/files/patch-scripts_ldmap.py deleted file mode 100644 index f9fb588048b1..000000000000 --- a/biology/haplohseq/files/patch-scripts_ldmap.py +++ /dev/null @@ -1,42 +0,0 @@ ---- scripts/ldmap.py.orig 2021-01-23 17:32:15 UTC -+++ scripts/ldmap.py -@@ -29,10 +29,10 @@ class MapMaker: - coordinates of the haplotype marker genomic positions. - ''' - def __init__(self, markerFilename, haplotypesFilename): -- print "reading haplotype base coordinates ...." -+ print("reading haplotype base coordinates ....") - self.coords, self.coordIndexes, self.refs, self.alts = self.readMarkers(markerFilename) - # self.haplotypes = self.readHaplotypes(haplotypesFilename) -- print "reading haplotype panel ...." -+ print("reading haplotype panel ....") - self.markerCalls = self.readHaplotypes(haplotypesFilename, transpose = True) - - # reads from a vcf file of defined positions representing the haplotype data -@@ -118,7 +118,7 @@ class MapMaker: - # 1) COLLECT MARGINALS AND IDENTIFY SITES THAT ARE POLYMORPHIC - # If a site has only one allele in the haplotype panel it is not informative, so it won't be used - # in LD calculations. We may want to consider setting some minimum threshold for a minor allele frequency. -- print "collecting marginal allele counts and identifying polymorphic sites from haplotype panel ...." -+ print("collecting marginal allele counts and identifying polymorphic sites from haplotype panel ....") - for index in range(0,len(self.markerCalls)): - ref = self.refs[index] - alt = self.alts[index] -@@ -152,7 +152,7 @@ class MapMaker: - log.write("Num non-polymorphic sites: " + str(numNonpolymorphicSites) + "\n") - - # 2) CALCULATE D FOR POLYMORPHIC SITES COMPARED WITH N SITES TO THE RIGHT THAT ARE POLYMORPHIC -- print "calculating D between polymorphic sites and their neighbors ...." -+ print("calculating D between polymorphic sites and their neighbors ....") - dVals = [] - for i in range(0, len(polymorphicIndexes)): # the last coordinate won't have any partners - index_i = polymorphicIndexes[i] -@@ -244,7 +244,7 @@ class LDMap: - return ldMap - - def save(self, filename): -- print "saving ldmap to " + filename -+ print("saving ldmap to " + filename) - ldMapFile = open(filename, 'w') - ldMapFile.write("\t".join(["COORD","REF","ALT","PAIRED_ALLELES"]) + "\n") - for i in range(0,len(self.coords)): diff --git a/biology/haplohseq/files/patch-scripts_simple__phaser.py b/biology/haplohseq/files/patch-scripts_simple__phaser.py deleted file mode 100644 index c6c5941ee00d..000000000000 --- a/biology/haplohseq/files/patch-scripts_simple__phaser.py +++ /dev/null @@ -1,31 +0,0 @@ ---- scripts/simple_phaser.py.orig 2021-01-23 17:25:56 UTC -+++ scripts/simple_phaser.py -@@ -108,7 +108,7 @@ class SimplePhaser: - return informativeHets, informativeCoords, informativeIndexes - - def getRefPairedAllele(self, anchorIndex, pairedIndex): --# print "\t".join([str(anchorIndex), str(pairedIndex - anchorIndex - 1), str(len(self.ldMap.dVals)),str(len(self.ldMap.dVals[anchorIndex]))]) # prints intermarker counts -+# print("\t".join([str(anchorIndex), str(pairedIndex - anchorIndex - 1), str(len(self.ldMap.dVals)),str(len(self.ldMap.dVals[anchorIndex]))]) # prints intermarker counts) - if (pairedIndex - anchorIndex - 1) >= len(self.ldMap.dVals[anchorIndex]): - pRef = random.uniform(0,1) - if pRef > 0.5: -@@ -166,8 +166,8 @@ class SimplePhaser: - altHap = temp - - if pairedAllele not in [ref,alt]: -- print "pairedAllele not ref or alt " + ref + " " + alt -- print pairedAllele -+ print("pairedAllele not ref or alt " + ref + " " + alt) -+ print(pairedAllele) - - return phasedAlleles, informativeCoords - -@@ -182,7 +182,7 @@ class SimplePhaser: - elif candidateHap[i].upper() == phasedHaps[1][i].upper(): - currentMatch = 1 - else: -- print "ERROR: " + candidateHap[i] + " does not match " + phasedHaps[0][i] + " or " + phasedHaps[1][i] + "\t" + self.ldMap.coords[i] + "\t" + self.ldMap.refs[i] + "\t" + self.ldMap.alts[i] -+ print("ERROR: " + candidateHap[i] + " does not match " + phasedHaps[0][i] + " or " + phasedHaps[1][i] + "\t" + self.ldMap.coords[i] + "\t" + self.ldMap.refs[i] + "\t" + self.ldMap.alts[i]) - # # randomly assign match - # p0 = random.uniform(0,1) - # if p0 > 0.5: diff --git a/biology/haplohseq/files/patch-src_FreqPhase.cpp b/biology/haplohseq/files/patch-src_FreqPhase.cpp deleted file mode 100644 index 9bab76aee2f5..000000000000 --- a/biology/haplohseq/files/patch-src_FreqPhase.cpp +++ /dev/null @@ -1,29 +0,0 @@ ---- src/FreqPhase.cpp.orig 2019-11-13 14:19:06 UTC -+++ src/FreqPhase.cpp -@@ -5,6 +5,7 @@ - * Email: sanlucas@gmail.com - */ - -+#include <sysexits.h> - #include "FreqPhase.h" - - namespace haplohseq { -@@ -180,10 +181,17 @@ double FreqPhase::meanValue(const std::v - double FreqPhase::medianValue(const std::vector<double>& values) { - double median; - size_t size = values.size(); -+ -+ // We can probably detect this condition earlier while loading the VCF -+ if ( size == 0 ) { -+ std::cerr << "FreqPhase::medianValue(): values vector is empty." << std::endl; -+ std::cerr << "Make sure your VCF has all of GT:AD:DP in the FORMAT column." << std::endl; -+ exit(EX_DATAERR); -+ } - std::vector<double> tempFreqs(values); - sort(tempFreqs.begin(), tempFreqs.end()); - -- if (size % 2 == 0) { -+ if (size % 2 == 0) { - median = (tempFreqs[size / 2 - 1] + tempFreqs[size / 2]) / 2; - } - else { diff --git a/biology/haplohseq/files/patch-src_HaplohSeq.cpp b/biology/haplohseq/files/patch-src_HaplohSeq.cpp deleted file mode 100644 index a80ce577f747..000000000000 --- a/biology/haplohseq/files/patch-src_HaplohSeq.cpp +++ /dev/null @@ -1,20 +0,0 @@ ---- src/HaplohSeq.cpp.orig 2019-09-01 14:58:30 UTC -+++ src/HaplohSeq.cpp -@@ -202,7 +202,7 @@ void HaplohSeq::runBafHaplohseq( std::string& obsType, - - // Spawn worker threads - for (std::size_t t = 0; t < numThreads; t++) { -- threadPool.create_thread(boost::bind((unsigned long int (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); -+ threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); - } - - std::map<std::string, boost::shared_ptr<Hmm> > chrHmms; -@@ -420,7 +420,7 @@ void HaplohSeq::runVcfHaplohseq( std::string& obsType, - - // Spawn worker threads - for (std::size_t t = 0; t < numThreads; t++) { -- threadPool.create_thread(boost::bind((unsigned long int (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); -+ threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); - } - - std::map<std::string, boost::shared_ptr<Hmm> > chrHmms; diff --git a/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp b/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp deleted file mode 100644 index 21ea56a8f600..000000000000 --- a/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- src/test/InputProcessorTest.cpp.orig 2019-09-01 12:33:22 UTC -+++ src/test/InputProcessorTest.cpp -@@ -82,7 +82,7 @@ BOOST_AUTO_TEST_CASE(isHetTest) { - BOOST_REQUIRE_EQUAL(inputProc.isHet('A','?'), false); - BOOST_REQUIRE_EQUAL(inputProc.isHet('A','.'), false); - BOOST_REQUIRE_EQUAL(inputProc.isHet('A',' '), false); -- BOOST_REQUIRE_EQUAL(inputProc.isHet('C', NULL), true); -+ BOOST_REQUIRE_EQUAL(inputProc.isHet('C','\0'), true); - } - - BOOST_AUTO_TEST_CASE(readAllelesTest) { diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile index 3d39f202a887..38ef7358c154 100644 --- a/biology/htslib/Makefile +++ b/biology/htslib/Makefile @@ -1,5 +1,5 @@ PORTNAME= htslib -DISTVERSION= 1.21 +DISTVERSION= 1.22 CATEGORIES= biology devel # Github generated distfiles are incomplete, so use custom tarball MASTER_SITES= https://github.com/samtools/htslib/releases/download/${DISTVERSION}/ @@ -15,7 +15,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libdeflate.so:archivers/libdeflate TEST_DEPENDS= bash:shells/bash -USES= autoreconf cpe gmake localbase pathfix perl5 shebangfix tar:bzip2 +USES= autoreconf cpe gmake localbase:ldflags pathfix perl5 shebangfix tar:bzip2 USE_PERL5= test USE_LDCONFIG= yes diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo index f035bfd3f3d0..fbe2d5f9d13e 100644 --- a/biology/htslib/distinfo +++ b/biology/htslib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1727437235 -SHA256 (htslib-1.21.tar.bz2) = 84b510e735f4963641f26fd88c8abdee81ff4cb62168310ae716636aac0f1823 -SIZE (htslib-1.21.tar.bz2) = 4781943 +TIMESTAMP = 1748951113 +SHA256 (htslib-1.22.tar.bz2) = 6250c1df297db477516e60ac8df45ed75a652d1f25b0f37f12f5b17269eafde9 +SIZE (htslib-1.22.tar.bz2) = 4830206 diff --git a/biology/htslib/pkg-plist b/biology/htslib/pkg-plist index 1d4e538f1e47..1825cfff6daf 100644 --- a/biology/htslib/pkg-plist +++ b/biology/htslib/pkg-plist @@ -1,6 +1,7 @@ bin/annot-tsv bin/bgzip bin/htsfile +bin/ref-cache bin/tabix include/htslib/bgzf.h include/htslib/cram.h @@ -38,6 +39,7 @@ libdata/pkgconfig/htslib.pc share/man/man1/annot-tsv.1.gz share/man/man1/bgzip.1.gz share/man/man1/htsfile.1.gz +share/man/man1/ref-cache.1.gz share/man/man1/tabix.1.gz share/man/man5/faidx.5.gz share/man/man5/sam.5.gz diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile index 55476ed67c9b..f281649f9c47 100644 --- a/biology/hyphy/Makefile +++ b/biology/hyphy/Makefile @@ -1,5 +1,5 @@ PORTNAME= hyphy -DISTVERSION= 2.5.70 +DISTVERSION= 2.5.73 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo index 7b906e8bb328..ae85017d004d 100644 --- a/biology/hyphy/distinfo +++ b/biology/hyphy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1742777609 -SHA256 (veg-hyphy-2.5.70_GH0.tar.gz) = 38c2549dcaec9f7df63b5e3aab965794484edc11a221fa0c0d909f7c68614de3 -SIZE (veg-hyphy-2.5.70_GH0.tar.gz) = 5617978 +TIMESTAMP = 1747240205 +SHA256 (veg-hyphy-2.5.73_GH0.tar.gz) = efc64adb9f270aa6c284dbee22a16132f4e59126e9df071c5267cd79e2883969 +SIZE (veg-hyphy-2.5.73_GH0.tar.gz) = 4161304 diff --git a/biology/hyphy/pkg-plist b/biology/hyphy/pkg-plist index 2f58e0cb50d2..cea5332c2742 100644 --- a/biology/hyphy/pkg-plist +++ b/biology/hyphy/pkg-plist @@ -11,6 +11,7 @@ bin/hyphy %%DATADIR%%/GeneticCodes/Thraustochytrium_mtDNA.cod %%DATADIR%%/GeneticCodes/Vertebratemtdna.cod %%DATADIR%%/GeneticCodes/Yeast_mtDNA.cod +%%DATADIR%%/README.md %%DATADIR%%/SubstitutionClasses/AAEFV/Equal %%DATADIR%%/SubstitutionClasses/AAEFV/Estimated %%DATADIR%%/SubstitutionClasses/AAEFV/Observed In Data Set @@ -177,6 +178,7 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/Samplers/srs-ErrorEst.ibf %%DATADIR%%/TemplateBatchFiles/Samplers/srs.ibf %%DATADIR%%/TemplateBatchFiles/SandNSAmbigs.bf +%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/BUSTED-PH.bf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FADE.bf @@ -333,7 +335,6 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/Utility/BranchLengthFitters.bf %%DATADIR%%/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf %%DATADIR%%/TemplateBatchFiles/Utility/CodonTools.bf -%%DATADIR%%/TemplateBatchFiles/Utility/DBTools.ibf %%DATADIR%%/TemplateBatchFiles/Utility/DescriptiveStatistics.bf %%DATADIR%%/TemplateBatchFiles/Utility/GrabBag.bf %%DATADIR%%/TemplateBatchFiles/Utility/HXB2Mapper.bf @@ -371,6 +372,10 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/globalChecker.ibf %%DATADIR%%/TemplateBatchFiles/heuristicMethodNPBootstrap.bf %%DATADIR%%/TemplateBatchFiles/last.date +%%DATADIR%%/TemplateBatchFiles/lib/label-tree.bf +%%DATADIR%%/TemplateBatchFiles/lib/remove-duplicates.bf +%%DATADIR%%/TemplateBatchFiles/lib/trim-label-tree.bf +%%DATADIR%%/TemplateBatchFiles/lib/trim-tree.bf %%DATADIR%%/TemplateBatchFiles/libv3/IOFunctions.bf %%DATADIR%%/TemplateBatchFiles/libv3/UtilityFunctions.bf %%DATADIR%%/TemplateBatchFiles/libv3/all-terms.bf @@ -393,6 +398,7 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV.bf %%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_MH.bf %%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf +%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES_BSREL.bf %%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_TRIP.bf %%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MSS.bf %%DATADIR%%/TemplateBatchFiles/libv3/models/frequencies.bf @@ -421,6 +427,7 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/libv3/tasks/mpi.bf %%DATADIR%%/TemplateBatchFiles/libv3/tasks/trees.bf %%DATADIR%%/TemplateBatchFiles/molclockBootstrap.bf +%%DATADIR%%/TemplateBatchFiles/molerate.bf %%DATADIR%%/TemplateBatchFiles/pairwiseDistanceEstimator.ibf %%DATADIR%%/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf %%DATADIR%%/TemplateBatchFiles/partitionSequences.ibf diff --git a/biology/iqtree/Makefile b/biology/iqtree/Makefile index 96543818f1ad..653f82c7f487 100644 --- a/biology/iqtree/Makefile +++ b/biology/iqtree/Makefile @@ -1,7 +1,7 @@ PORTNAME= iqtree DISTVERSIONPREFIX= v DISTVERSION= 2.4.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index 91193aa7facc..ee2b20397ca6 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -1,6 +1,7 @@ PORTNAME= kallisto DISTVERSIONPREFIX= v DISTVERSION= 0.51.1 +PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= biology @@ -37,6 +38,7 @@ CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON -DUSE_BAM:BOOL=ON # WIP: Remove before committing CMAKE_ARGS+= -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON MAKE_JOBS_UNSAFE= yes +CXXFLAGS+= -Wno-unqualified-std-cast-call LDFLAGS+= -lhts -lz OPTIONS_DEFINE= EXAMPLES diff --git a/biology/kallisto/distinfo b/biology/kallisto/distinfo index 98b8775d9539..a207db3e922d 100644 --- a/biology/kallisto/distinfo +++ b/biology/kallisto/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1726658334 +TIMESTAMP = 1748283025 SHA256 (pachterlab-kallisto-v0.51.1_GH0.tar.gz) = a8bcc23bca6ac758f15e30bb77e9e169e628beff2da3be2e34a53e1d42253516 SIZE (pachterlab-kallisto-v0.51.1_GH0.tar.gz) = 5954250 diff --git a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt index d25cf028cfdd..c662b37881c9 100644 --- a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt +++ b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt @@ -1,8 +1,8 @@ ---- ext/bifrost/CMakeLists.txt.orig 2023-06-27 10:45:00 UTC +--- ext/bifrost/CMakeLists.txt.orig 2024-09-17 05:40:08 UTC +++ ext/bifrost/CMakeLists.txt -@@ -7,18 +7,12 @@ find_package(Threads REQUIRED) +@@ -6,18 +6,12 @@ SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX + # To enable a larger default k-mer size, replace MAX_KMER_SIZE with a larger multiple of 32: actual maximum k-mer size will be MAX_KMER_SIZE-1. - SET(MAX_KMER_SIZE "32" CACHE STRING "MAX_KMER_SIZE") SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX_GMER_SIZE") -# Enable architecture optimizations -SET(COMPILATION_ARCH "native" CACHE STRING "COMPILATION_ARCH") @@ -12,7 +12,8 @@ # Set some default compile flags set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c11") - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") +-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") ++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wno-unqualified-std-cast-call") -set_property(SOURCE BlockedBloomFilter.cpp APPEND_STRING PROPERTY COMPILE_FLAGS " -funroll-loops") - @@ -20,7 +21,7 @@ #check if we are on arm64 and apple, if so, disable AVX2 if(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm") message("Disabling AVX2 instructions on arm64") -@@ -30,8 +24,6 @@ if(COMPILATION_ARCH MATCHES "OFF") +@@ -29,8 +23,6 @@ else(COMPILATION_ARCH MATCHES "OFF") message("Disabling native architecture compilation (including AVX2)") else(COMPILATION_ARCH MATCHES "OFF") message("Compilation architecture: ${COMPILATION_ARCH}") @@ -29,7 +30,7 @@ endif(COMPILATION_ARCH MATCHES "OFF") if(ENABLE_AVX2 MATCHES "OFF") -@@ -56,7 +48,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug) +@@ -55,7 +47,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug) set(CMAKE_EXE_LINKER_FLAGS "-pg") else(CMAKE_BUILD_TYPE MATCHES Profile) message("Build type: Release") diff --git a/biology/kallisto/files/patch-ext_bifrost_src_DataStorage.tcc b/biology/kallisto/files/patch-ext_bifrost_src_DataStorage.tcc new file mode 100644 index 000000000000..0e6dcb8cca18 --- /dev/null +++ b/biology/kallisto/files/patch-ext_bifrost_src_DataStorage.tcc @@ -0,0 +1,14 @@ +--- ext/bifrost/src/DataStorage.tcc.orig 2024-09-17 05:40:08 UTC ++++ ext/bifrost/src/DataStorage.tcc +@@ -78,7 +78,10 @@ DataStorage<U>::DataStorage(const DataStorage& o) : co + + unitig_cs_link = new atomic<uint64_t>[sz_link]; + +- for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load(); ++ // Hayzam Sherif: o.sz_link -> o.unitig_cs_link ++ // Independently proposed by Lucas van Dijk: ++ // https://github.com/pmelsted/bifrost/pull/18/files ++ for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.unitig_cs_link[i].load(); + } + + if ((o.data != nullptr) && (o.sz_cs != 0)){ diff --git a/biology/kmcp/Makefile b/biology/kmcp/Makefile index d52bac6491ea..edf21fc0a1c7 100644 --- a/biology/kmcp/Makefile +++ b/biology/kmcp/Makefile @@ -1,7 +1,7 @@ PORTNAME= kmcp DISTVERSIONPREFIX= v DISTVERSION= 0.9.4 -PORTREVISION= 10 +PORTREVISION= 12 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/lamarc/Makefile b/biology/lamarc/Makefile index 46f4e102635a..ad200a6ffe56 100644 --- a/biology/lamarc/Makefile +++ b/biology/lamarc/Makefile @@ -1,25 +1,25 @@ PORTNAME= lamarc PORTVERSION= 2.1.8 DISTVERSIONSUFFIX= -src -PORTREVISION= 1 +PORTREVISION= 2 PORTEPOCH= 1 CATEGORIES= biology MASTER_SITES= http://evolution.genetics.washington.edu/lamarc/download/ -MAINTAINER= ports@FreeBSD.org +MAINTAINER= hayzam@alchemilla.io COMMENT= Package of programs for computing population parameters WWW= https://evolution.genetics.washington.edu/lamarc/ LICENSE= APACHE20 -BROKEN_FreeBSD_14= fails to compile: no matching function for call to 'make_pair' - USE_CXXSTD= c++98 GNU_CONFIGURE= yes WRKSRC= ${WRKDIR}/${DISTNAME:S,${DISTVERSIONSUFFIX},,} +CXXFLAGS+= -Wno-unused-parameter -Wno-mismatched-tags + PLIST_FILES= bin/${PORTNAME} PORTDOCS= * diff --git a/biology/lamarc/files/patch-src_control_chainmanager.cpp b/biology/lamarc/files/patch-src_control_chainmanager.cpp new file mode 100644 index 000000000000..bf21359154ab --- /dev/null +++ b/biology/lamarc/files/patch-src_control_chainmanager.cpp @@ -0,0 +1,11 @@ +--- src/control/chainmanager.cpp.orig 2025-05-18 23:57:13 UTC ++++ src/control/chainmanager.cpp +@@ -1631,7 +1631,7 @@ vector<pair<double, long int> > ChainManager::SortChai + unsigned long int i; + for (i = 0; i < temps.size(); ++i) + { +- orderedtemps.push_back(make_pair<double, long int>(temps[i].GetTemperature(), i)); ++ orderedtemps.push_back(make_pair(temps[i].GetTemperature(), i)); + } + std::sort(orderedtemps.begin(), orderedtemps.end()); + return orderedtemps; diff --git a/biology/lamarc/files/patch-src_tools_mathx.cpp b/biology/lamarc/files/patch-src_tools_mathx.cpp new file mode 100644 index 000000000000..527dfe4af344 --- /dev/null +++ b/biology/lamarc/files/patch-src_tools_mathx.cpp @@ -0,0 +1,11 @@ +--- src/tools/mathx.cpp.orig 2025-05-19 00:00:29 UTC ++++ src/tools/mathx.cpp +@@ -778,7 +778,7 @@ std::pair<DoubleVec1d, DoubleVec2d> EigenCalculator::E + { + eigvals[i] = a[i][i]; + } +- return std::make_pair<DoubleVec1d, DoubleVec2d>(eigvals, eigvecs); ++ return std::make_pair(eigvals, eigvecs); + } // Eigen + + //------------------------------------------------------------------------------------ diff --git a/biology/lamarc/files/patch-src_tools_stringx.h b/biology/lamarc/files/patch-src_tools_stringx.h index d1ded1a7d8da..04019393fbac 100644 --- a/biology/lamarc/files/patch-src_tools_stringx.h +++ b/biology/lamarc/files/patch-src_tools_stringx.h @@ -1,6 +1,6 @@ --- src/tools/stringx.h.orig 2011-04-23 02:02:49 UTC +++ src/tools/stringx.h -@@ -107,6 +107,26 @@ struct CIStringCompare : public std::bin +@@ -107,6 +107,26 @@ bool ciStringEqual(const std::string& s1, const std::s bool ciStringEqual(const std::string& s1, const std::string& s2); @@ -27,10 +27,11 @@ //------------------------------------------------------------------------------------ template <class T> -@@ -188,26 +208,6 @@ bool FromString(const std::string & in, +@@ -187,26 +207,6 @@ DoubleVec1d StringToDoubleVecOrBarf(const std::string& + bool FromString(const std::string & in, method_type& out); DoubleVec1d StringToDoubleVecOrBarf(const std::string& in); - +- -// functions for making xmltags and lines of xml -std::string MakeTag(const std::string& str); -std::string MakeCloseTag(const std::string& str); @@ -50,7 +51,6 @@ -std::string Pretty(long number, int width=DEFWIDTH); -std::string Pretty(unsigned long number, int width=DEFWIDTH); -std::string Pretty(std::string str, int width=DEFWIDTH); -- + bool StringCompare(const std::string&, const char*, long, long); bool StringCompare(const std::string&, const std::string&, long, long); - diff --git a/biology/lamarc/files/patch-src_tree_arrangervec.cpp b/biology/lamarc/files/patch-src_tree_arrangervec.cpp new file mode 100644 index 000000000000..ff3636f3a571 --- /dev/null +++ b/biology/lamarc/files/patch-src_tree_arrangervec.cpp @@ -0,0 +1,11 @@ +--- src/tree/arrangervec.cpp.orig 2025-05-18 23:55:20 UTC ++++ src/tree/arrangervec.cpp +@@ -116,7 +116,7 @@ void ArrangerVec::CopyAllMembers(const ArrangerVec & c + for(it = cp.arrangers.begin(); it != cp.arrangers.end(); it++) + { + Arranger* arr = (*it).second->Clone(); +- arrangers.insert(std::make_pair<string, Arranger*>(arr->GetName(), arr)); ++ arrangers.insert(std::make_pair(arr->GetName(), arr)); + } + } + } diff --git a/biology/lamarc/files/patch-src_tree_collector.cpp b/biology/lamarc/files/patch-src_tree_collector.cpp new file mode 100644 index 000000000000..bff56a70b261 --- /dev/null +++ b/biology/lamarc/files/patch-src_tree_collector.cpp @@ -0,0 +1,11 @@ +--- src/tree/collector.cpp.orig 2025-05-18 23:58:39 UTC ++++ src/tree/collector.cpp +@@ -204,7 +204,7 @@ void ParamCollector::AddParamSummary(ForceParameters f + + void ParamCollector::AddParamSummary(ForceParameters fp, long ncopy) + { +- m_paramsum.push_back(make_pair<ForceParameters, long>(fp, ncopy)); ++ m_paramsum.push_back(std::make_pair(fp, ncopy)); + } + + //------------------------------------------------------------------------------------ diff --git a/biology/lamarc/files/patch-src_tree_prior.cpp b/biology/lamarc/files/patch-src_tree_prior.cpp new file mode 100644 index 000000000000..a8dbf7ab04ed --- /dev/null +++ b/biology/lamarc/files/patch-src_tree_prior.cpp @@ -0,0 +1,17 @@ +--- src/tree/prior.cpp.orig 2025-05-18 23:58:05 UTC ++++ src/tree/prior.cpp +@@ -85,12 +85,12 @@ std::pair<double, double> Prior::RandomDraw() const + case LINEAR: + newparam = rnd.Float() * (m_upperbound - m_lowerbound) + m_lowerbound; + newlnparam = log(newparam); +- return std::make_pair<double, double>(newparam, newlnparam); ++ return std::make_pair(newparam, newlnparam); + break; + case LOGARITHMIC: + newlnparam = rnd.Float() * (m_lnupper - m_lnlower) + m_lnlower; + newparam = exp(newlnparam); +- return std::make_pair<double, double>(newparam, newlnparam); ++ return std::make_pair(newparam, newlnparam); + break; + } + string e = "Unknown prior type " + ToString(m_priortype) + diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile index 383b06145b85..fec0997b39be 100644 --- a/biology/libsbml/Makefile +++ b/biology/libsbml/Makefile @@ -1,7 +1,6 @@ PORTNAME= libsbml -PORTVERSION= 5.20.4 +PORTVERSION= 5.20.5 DISTVERSIONPREFIX= v -PORTREVISION= 1 CATEGORIES= biology devel MAINTAINER= sunpoet@FreeBSD.org @@ -74,7 +73,6 @@ post-patch: @${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|g' ${WRKSRC}/CMakeLists.txt post-install-EXAMPLES-on: - ${MV} ${STAGEDIR}${DATADIR}/examples ${STAGEDIR}${EXAMPLESDIR} - ${RMDIR} ${STAGEDIR}${DATADIR} + ${MV} ${STAGEDIR}${DATADIR}examples ${STAGEDIR}${EXAMPLESDIR} .include <bsd.port.mk> diff --git a/biology/libsbml/distinfo b/biology/libsbml/distinfo index 7884ce4f4a5c..7908d7960b79 100644 --- a/biology/libsbml/distinfo +++ b/biology/libsbml/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1725559551 -SHA256 (sbmlteam-libsbml-v5.20.4_GH0.tar.gz) = 02c225d3513e1f5d6e3c0168456f568e67f006eddaab82f09b4bdf0d53d2050e -SIZE (sbmlteam-libsbml-v5.20.4_GH0.tar.gz) = 28796139 +TIMESTAMP = 1747546406 +SHA256 (sbmlteam-libsbml-v5.20.5_GH0.tar.gz) = 21c88c753a4a031f157a033de3810488b86f003e684c6ca7aa3d6e26e7e0acfc +SIZE (sbmlteam-libsbml-v5.20.5_GH0.tar.gz) = 28852940 diff --git a/biology/libsbml/files/patch-CMakeLists.txt b/biology/libsbml/files/patch-CMakeLists.txt index 037277324c79..32366d12deb1 100644 --- a/biology/libsbml/files/patch-CMakeLists.txt +++ b/biology/libsbml/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2023-04-03 10:48:28 UTC +--- CMakeLists.txt.orig 2025-05-05 04:53:07 UTC +++ CMakeLists.txt -@@ -430,8 +430,6 @@ if(WITH_EXPAT) +@@ -445,8 +445,6 @@ if(WITH_EXPAT) set(LIBSBML_XML_LIBRARY_INCLUDE ${EXPAT_INCLUDE_DIR}) set(LIBSBML_XML_LIBRARY_LIBS ${EXPAT_LIBRARY}) @@ -9,7 +9,7 @@ endif(WITH_EXPAT) -@@ -452,8 +450,6 @@ if(WITH_LIBXML) +@@ -467,8 +465,6 @@ if(WITH_LIBXML) set(LIBSBML_XML_LIBRARY_INCLUDE ${LIBXML_INCLUDE_DIR}) set(LIBSBML_XML_LIBRARY_LIBS ${LIBXML_LIBRARY}) @@ -18,7 +18,7 @@ endif(WITH_LIBXML) -@@ -473,8 +469,6 @@ if(WITH_XERCES) +@@ -488,8 +484,6 @@ if(WITH_XERCES) set(LIBSBML_XML_LIBRARY_INCLUDE ${XERCES_INCLUDE_DIR}) set(LIBSBML_XML_LIBRARY_LIBS ${XERCES_LIBRARY}) @@ -27,7 +27,7 @@ endif(WITH_XERCES) ############################################################################### -@@ -498,7 +492,6 @@ if(WITH_BZIP2) +@@ -513,7 +507,6 @@ if(WITH_BZIP2) set(USE_BZ2 ON) add_definitions( -DUSE_BZ2 ) list(APPEND SWIG_EXTRA_ARGS -DUSE_BZ2) @@ -35,16 +35,16 @@ endif(WITH_BZIP2) -@@ -608,8 +601,6 @@ valid. It should contain the file zlib.h, but it does - INTERFACE_INCLUDE_DIRECTORIES "${LIBZ_INCLUDE_DIR}") - endif() - +@@ -550,8 +543,6 @@ if(WITH_ZLIB) + set(USE_ZLIB ON) + add_definitions( -DUSE_ZLIB ) + list(APPEND SWIG_EXTRA_ARGS -DUSE_ZLIB) - list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindZLIB.cmake") - endif(WITH_ZLIB) # install find scripts only for used dependencies -@@ -981,22 +972,6 @@ if(WITH_DOXYGEN) +@@ -923,20 +914,6 @@ endif() add_subdirectory(docs) endif() @@ -62,8 +62,6 @@ - README.md - VERSION.txt -) -- --install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX}) - ############################################################################### - # + install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX}) + diff --git a/biology/libsbml/pkg-plist b/biology/libsbml/pkg-plist index 7a382979c5e4..df36c508c663 100644 --- a/biology/libsbml/pkg-plist +++ b/biology/libsbml/pkg-plist @@ -107,6 +107,31 @@ include/sbml/extension/SBaseExtensionPoint.h include/sbml/extension/SBasePlugin.h include/sbml/extension/SBasePluginCreator.h include/sbml/extension/SBasePluginCreatorBase.h +include/sbml/html2md/html2md.h +include/sbml/html2md/table.h +include/sbml/maddy/blockparser.h +include/sbml/maddy/breaklineparser.h +include/sbml/maddy/checklistparser.h +include/sbml/maddy/codeblockparser.h +include/sbml/maddy/emphasizedparser.h +include/sbml/maddy/headlineparser.h +include/sbml/maddy/horizontallineparser.h +include/sbml/maddy/htmlparser.h +include/sbml/maddy/imageparser.h +include/sbml/maddy/inlinecodeparser.h +include/sbml/maddy/italicparser.h +include/sbml/maddy/latexblockparser.h +include/sbml/maddy/lineparser.h +include/sbml/maddy/linkparser.h +include/sbml/maddy/orderedlistparser.h +include/sbml/maddy/paragraphparser.h +include/sbml/maddy/parser.h +include/sbml/maddy/parserconfig.h +include/sbml/maddy/quoteparser.h +include/sbml/maddy/strikethroughparser.h +include/sbml/maddy/strongparser.h +include/sbml/maddy/tableparser.h +include/sbml/maddy/unorderedlistparser.h include/sbml/math/ASTNode.h include/sbml/math/ASTNodeType.h include/sbml/math/DefinitionURLRegistry.h @@ -236,6 +261,7 @@ share/cmake/Modules/FindLIBSBML.cmake %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/createExampleSBML.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/echoSBML.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/getAllElementsWithNotes.cpp +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inferReactions.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inferUnits.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inlineFunctionDefintions.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printAnnotation.cpp diff --git a/biology/linux-foldingathome/Makefile b/biology/linux-foldingathome/Makefile index 93c320c4176c..b9948103d97d 100644 --- a/biology/linux-foldingathome/Makefile +++ b/biology/linux-foldingathome/Makefile @@ -4,7 +4,6 @@ CATEGORIES= biology linux MASTER_SITES= https://download.foldingathome.org/releases/public/fah-client/debian-10-64bit/release/ PKGNAMEPREFIX= linux- DISTNAME= fah-client_${DISTVERSION}-64bit-release -EXTRACT_SUFX= .tar.bz2 MAINTAINER= 0mp@FreeBSD.org COMMENT= Folding@home Client @@ -20,7 +19,7 @@ LICENSE_PERMS= no-dist-mirror no-dist-sell no-pkg-mirror no-pkg-sell \ ONLY_FOR_ARCHS= amd64 ONLY_FOR_ARCHS_REASON= has not been ported to this architecture -USES= linux:rl9 +USES= linux:rl9 tar:bz2 USE_LINUX= systemd-libs USE_RC_SUBR= fahclient diff --git a/biology/megahit/Makefile b/biology/megahit/Makefile index 379440059baa..164ef21acf64 100644 --- a/biology/megahit/Makefile +++ b/biology/megahit/Makefile @@ -1,7 +1,7 @@ PORTNAME= megahit DISTVERSIONPREFIX= v -DISTVERSION= 1.2.9 -PORTREVISION= 1 +DISTVERSION= 1.2.9-20 +DISTVERSIONSUFFIX= -g3821b10 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -11,8 +11,8 @@ WWW= https://github.com/voutcn/megahit LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE -ONLY_FOR_ARCHS= amd64 powerpc64 powerpc64le riscv64 -ONLY_FOR_ARCHS_REASON= "Uses specific 64-bit CPU features" +ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le riscv64 +ONLY_FOR_ARCHS_REASON= Requires a 64-bit processor USES= cmake python shebangfix SHEBANG_FILES= src/megahit diff --git a/biology/megahit/distinfo b/biology/megahit/distinfo index a70a74294d7a..eaf38afd5db0 100644 --- a/biology/megahit/distinfo +++ b/biology/megahit/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1669058254 -SHA256 (voutcn-megahit-v1.2.9_GH0.tar.gz) = 09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852 -SIZE (voutcn-megahit-v1.2.9_GH0.tar.gz) = 268591 +TIMESTAMP = 1748000175 +SHA256 (voutcn-megahit-v1.2.9-20-g3821b10_GH0.tar.gz) = 743d45843a4fb58134c1e68e5d5e0987320bc3dfa949f1ab6e719b78d1f317fa +SIZE (voutcn-megahit-v1.2.9-20-g3821b10_GH0.tar.gz) = 268974 diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile index eb65d48578c5..dd10b6869afe 100644 --- a/biology/minimap2/Makefile +++ b/biology/minimap2/Makefile @@ -1,6 +1,6 @@ PORTNAME= minimap2 DISTVERSIONPREFIX= v -DISTVERSION= 2.29 +DISTVERSION= 2.30 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/minimap2/distinfo b/biology/minimap2/distinfo index fac01c43c7f5..f7c616549712 100644 --- a/biology/minimap2/distinfo +++ b/biology/minimap2/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1745154104 -SHA256 (lh3-minimap2-v2.29_GH0.tar.gz) = 008d5e9848b918e4eb09d054aa3d6c272d50e92b8fc8537abf5081a507019718 -SIZE (lh3-minimap2-v2.29_GH0.tar.gz) = 269107 +TIMESTAMP = 1750076274 +SHA256 (lh3-minimap2-v2.30_GH0.tar.gz) = 4e5cd621be2b2685c5c88d9b9b169c7e036ab9fff2f3afe1a1d4091ae3176380 +SIZE (lh3-minimap2-v2.30_GH0.tar.gz) = 269912 diff --git a/biology/minimap2/pkg-plist b/biology/minimap2/pkg-plist index 742d1eb1b3f7..9e386df64f48 100644 --- a/biology/minimap2/pkg-plist +++ b/biology/minimap2/pkg-plist @@ -8,3 +8,6 @@ share/man/man1/minimap2.1.gz %%DATADIR%%/test/q2.fa %%DATADIR%%/test/t-inv.fa %%DATADIR%%/test/t2.fa +%%DATADIR%%/test/x3s-aln.txt +%%DATADIR%%/test/x3s-qry.fa +%%DATADIR%%/test/x3s-ref.fa diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile index b87a9c2d6b60..bf3541b88534 100644 --- a/biology/ncbi-blast+/Makefile +++ b/biology/ncbi-blast+/Makefile @@ -1,6 +1,6 @@ PORTNAME= ncbi-blast+ DISTVERSION= 2.16.0 -PORTREVISION= 3 +PORTREVISION= 5 CATEGORIES= biology perl5 python MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ diff --git a/biology/ncbi-entrez-direct/Makefile b/biology/ncbi-entrez-direct/Makefile index 43ccbb2354ba..881bd2e8b7e1 100644 --- a/biology/ncbi-entrez-direct/Makefile +++ b/biology/ncbi-entrez-direct/Makefile @@ -1,6 +1,6 @@ PORTNAME= ncbi-entrez-direct DISTVERSION= 14.9.20210423 -PORTREVISION= 26 +PORTREVISION= 28 CATEGORIES= biology perl5 MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/${PORTVERSION}/ DISTFILES= edirect.tar.gz diff --git a/biology/p5-TrimGalore/Makefile b/biology/p5-TrimGalore/Makefile index 8b6e229c0032..cd7a5cf7ffe7 100644 --- a/biology/p5-TrimGalore/Makefile +++ b/biology/p5-TrimGalore/Makefile @@ -3,7 +3,7 @@ DISTVERSION= 0.6.10 CATEGORIES= biology perl5 python PKGNAMEPREFIX= p5- -MAINTAINER= ports@FreeBSD.org +MAINTAINER= perl@FreeBSD.org COMMENT= Wrapper around Cutadapt and FastQC for adapter and quality trimming WWW= https://github.com/FelixKrueger/TrimGalore diff --git a/biology/paml/Makefile b/biology/paml/Makefile index 7ba18e506f72..4a6375689d5e 100644 --- a/biology/paml/Makefile +++ b/biology/paml/Makefile @@ -1,5 +1,6 @@ PORTNAME= paml -DISTVERSION= 4.10.7 +DISTVERSIONPREFIX= v +DISTVERSION= 4.10.9 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org diff --git a/biology/paml/distinfo b/biology/paml/distinfo index cd64f0e34127..7dd47591a370 100644 --- a/biology/paml/distinfo +++ b/biology/paml/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1688759942 -SHA256 (abacus-gene-paml-4.10.7_GH0.tar.gz) = 0f29e768b3797b69eadc6332c3d046d8727702052d56c3b729883626c0a5a4e3 -SIZE (abacus-gene-paml-4.10.7_GH0.tar.gz) = 5250841 +TIMESTAMP = 1747232666 +SHA256 (abacus-gene-paml-v4.10.9_GH0.tar.gz) = 19ca9d484d729324748b9c86453e4c8f4a1fa79ad6fa3ac7cdbfaa7d0bfb8c22 +SIZE (abacus-gene-paml-v4.10.9_GH0.tar.gz) = 3920159 diff --git a/biology/paml/files/patch-src_Makefile b/biology/paml/files/patch-src_Makefile index 4a9bd7ed2da6..1fd048a0594b 100644 --- a/biology/paml/files/patch-src_Makefile +++ b/biology/paml/files/patch-src_Makefile @@ -1,10 +1,11 @@ ---- src/Makefile.orig 2023-07-08 03:40:50 UTC +--- src/Makefile.orig 2025-05-14 14:29:51 UTC +++ src/Makefile -@@ -1,6 +1,6 @@ CC = cc # cc, gcc, cl +@@ -1,6 +1,6 @@ PRGS = baseml codeml basemlg mcmctree pamp evolver yn PRGS = baseml codeml basemlg mcmctree pamp evolver yn00 chi2 - CC = cc # cc, gcc, cl --CFLAGS = -O3 -Wall -Wno-unused-result -Wmemset-elt-size -+CFLAGS = -O3 -Wall -Wno-unused-result - #CC = icc - #CFLAGS = -fast -Wall +-CC = gcc +-CFLAGS = -O3 -Wall -Wno-unused-variable -Wno-unused-result ++#CC = gcc ++#CFLAGS = -O3 -Wall -Wno-unused-variable -Wno-unused-result + + LIBS = -lm diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist index 544b761367c3..02f053d2563e 100644 --- a/biology/paml/pkg-plist +++ b/biology/paml/pkg-plist @@ -199,8 +199,6 @@ bin/yn00 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/data-MCU0.95-rep1.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/mlb-nhomo4.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/mlb-nhomo5.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/rst-nhomo4.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/rst-nhomo5.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/tree-nhomo4.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/tree-nhomo5.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl diff --git a/biology/pbbam/Makefile b/biology/pbbam/Makefile index 197982227dff..830fbf557364 100644 --- a/biology/pbbam/Makefile +++ b/biology/pbbam/Makefile @@ -1,6 +1,6 @@ PORTNAME= pbbam DISTVERSION= 0.18.0 # Test with biology/unanimity before upgrading! -PORTREVISION= 11 +PORTREVISION= 12 CATEGORIES= biology # As of March 2018, unanimity is no longer open source. diff --git a/biology/py-biosig/Makefile b/biology/py-biosig/Makefile index fef5dc890c22..b1eaac088600 100644 --- a/biology/py-biosig/Makefile +++ b/biology/py-biosig/Makefile @@ -28,6 +28,6 @@ post-patch: ${TOUCH} README.md post-install: - @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/biosig${PYTHON_EXT_SUFFIX}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/biosig${PYTHON_TAG}.so .include <bsd.port.mk> diff --git a/biology/py-cutadapt/Makefile b/biology/py-cutadapt/Makefile index d787dcd42a55..c9963c7c1ef4 100644 --- a/biology/py-cutadapt/Makefile +++ b/biology/py-cutadapt/Makefile @@ -1,6 +1,5 @@ PORTNAME= cutadapt -DISTVERSION= 5.0 -PORTREVISION= 1 +DISTVERSION= 5.1 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/py-cutadapt/distinfo b/biology/py-cutadapt/distinfo index 1613aa2d6c1a..98c60c1e3018 100644 --- a/biology/py-cutadapt/distinfo +++ b/biology/py-cutadapt/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1736523245 -SHA256 (cutadapt-5.0.tar.gz) = cd66872b6635c068cf223f72fb0cc93b2454088a3e807a550bb36f717d25ae29 -SIZE (cutadapt-5.0.tar.gz) = 251297 +TIMESTAMP = 1749206212 +SHA256 (cutadapt-5.1.tar.gz) = 6bc76345c0a45f6b680cb1164e48eb1f81815c764ec471284ab6234c6653b937 +SIZE (cutadapt-5.1.tar.gz) = 252843 diff --git a/biology/py-cutadapt/files/patch-pyprojetc.toml b/biology/py-cutadapt/files/patch-pyprojetc.toml new file mode 100644 index 000000000000..7a3ad00ad87c --- /dev/null +++ b/biology/py-cutadapt/files/patch-pyprojetc.toml @@ -0,0 +1,11 @@ +--- pyproject.toml.orig 2025-06-06 12:32:50.569385000 +0200 ++++ pyproject.toml 2025-06-06 12:33:10.984604000 +0200 +@@ -9,7 +9,7 @@ + ] + description = "Adapter trimming and other preprocessing of high-throughput sequencing reads" + readme = "README.rst" +-license = "MIT" ++license = {text = "MIT"} + classifiers = [ + "Development Status :: 5 - Production/Stable", + "Environment :: Console", diff --git a/biology/py-orange3-bioinformatics/Makefile b/biology/py-orange3-bioinformatics/Makefile deleted file mode 100644 index 7904ed980863..000000000000 --- a/biology/py-orange3-bioinformatics/Makefile +++ /dev/null @@ -1,35 +0,0 @@ -PORTNAME= orange3-bioinformatics -DISTVERSION= 4.8.4 -PORTREVISION= 1 -CATEGORIES= biology python -MASTER_SITES= PYPI -PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} -DISTNAME= ${PORTNAME:S/-/_/}-${DISTVERSION} - -MAINTAINER= yuri@FreeBSD.org -COMMENT= Orange add-on providing common functionality for bioinformatics -WWW= https://github.com/biolab/orange3-bioinformatics/ - -LICENSE= GPLv3 -LICENSE_FILE= ${WRKSRC}/LICENSE - -DEPRECATED= Depends on expiring misc/orange3 -EXPIRATION_DATE=2025-06-21 - -BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} -RUN_DEPENDS= orange3>0:misc/orange3 \ - ${PYTHON_PKGNAMEPREFIX}Genesis-PyAPI>0:biology/py-Genesis-PyAPI@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}point-annotator>=2.0:math/py-point-annotator@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pyclipper>=1.2.0:math/py-pyclipper@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}requests>0:www/py-requests@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}requests-cache0>0:www/py-requests-cache0@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}resdk>0:biology/py-resdk@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scipy>=1.5.0:science/py-scipy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}serverfiles>0:misc/py-serverfiles@${PY_FLAVOR} - -USES= python -USE_PYTHON= autoplist distutils - -NO_ARCH= yes - -.include <bsd.port.mk> diff --git a/biology/py-orange3-bioinformatics/distinfo b/biology/py-orange3-bioinformatics/distinfo deleted file mode 100644 index 4b386c48e193..000000000000 --- a/biology/py-orange3-bioinformatics/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1739870048 -SHA256 (orange3_bioinformatics-4.8.4.tar.gz) = 275a32d3948df5294350c25bb430336b5d4109afaf71edd7ccc76591cb9eeb8b -SIZE (orange3_bioinformatics-4.8.4.tar.gz) = 3736720 diff --git a/biology/py-orange3-bioinformatics/pkg-descr b/biology/py-orange3-bioinformatics/pkg-descr deleted file mode 100644 index 8979fa28157a..000000000000 --- a/biology/py-orange3-bioinformatics/pkg-descr +++ /dev/null @@ -1,9 +0,0 @@ -Orange Bioinformatics extends Orange, a data mining software package, with -common functionality for bioinformatics. The provided functionality can be -accessed as a Python library or through a visual programming interface (Orange -Canvas). The latter is also suitable for non-programmers. - -Orange Bioinformatics provides access to publicly available data, like GEO data -sets, GO and KEGG. All features can be combined with powerful visualization, -network exploration and data mining techniques from the Orange data mining -framework. diff --git a/biology/py-orange3-single-cell/Makefile b/biology/py-orange3-single-cell/Makefile deleted file mode 100644 index 6a639bd90bbc..000000000000 --- a/biology/py-orange3-single-cell/Makefile +++ /dev/null @@ -1,46 +0,0 @@ -PORTNAME= orange3-single-cell -DISTVERSION= 0.8.2 -PORTREVISION= 6 -CATEGORIES= biology python -PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} - -MAINTAINER= yuri@FreeBSD.org -COMMENT= Orange add-on for gene expression of single cell data -WWW= https://singlecell.biolab.si/ - -LICENSE= AGPLv3+ - -DEPRECATED= Depends on expired math/py-fastdtw and expiring misc/orange3 -EXPIRATION_DATE=2025-06-01 - -RUN_DEPENDS= orange3>0:misc/orange3 \ - ${PYTHON_PKGNAMEPREFIX}orange3-bioinformatics>0:biology/py-orange3-bioinformatics@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}astropy>0:astro/py-astropy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}fastdtw>0:math/py-fastdtw@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}joblib>=0.11:devel/py-joblib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}loompy>=2.0.10:biology/py-loompy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}networkx>0:math/py-networkx@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pandas>=0.23:math/py-pandas@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scikit-learn>0:science/py-scikit-learn@${PY_FLAVOR} \ - ${PYNUMPY} - -# Supports 3.4+ but loompy 3.6+ only. -USES= python -USE_GITHUB= yes -GH_ACCOUNT= biolab -USE_PYTHON= distutils autoplist - -NO_ARCH= yes - -OPTIONS_DEFINE= DOCS - -DOCS_BUILD_DEPENDS= gmake:devel/gmake \ - ${PYTHON_PKGNAMEPREFIX}sphinx>=0,1:textproc/py-sphinx@${PY_FLAVOR} - -pre-build-DOCS-on: - @cd ${WRKSRC}/doc && ${SETENV} ${MAKE_ENV} ${GMAKE} html htmlhelp SPHINXBUILD=${LOCALBASE}/bin/sphinx-build-${PYTHON_VER} - -pre-build-DOCS-off: - @${REINPLACE_CMD} "s|^ include_documentation| #include_documentation|" ${WRKSRC}/setup.py - -.include <bsd.port.mk> diff --git a/biology/py-orange3-single-cell/distinfo b/biology/py-orange3-single-cell/distinfo deleted file mode 100644 index ed5f301ce6e1..000000000000 --- a/biology/py-orange3-single-cell/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1539761270 -SHA256 (biolab-orange3-single-cell-0.8.2_GH0.tar.gz) = eebda4303c208951fcbe8f383e0f310b20abedba425b0c68bbe65ae2806cc1bb -SIZE (biolab-orange3-single-cell-0.8.2_GH0.tar.gz) = 5521782 diff --git a/biology/py-orange3-single-cell/files/patch-doc_conf.py b/biology/py-orange3-single-cell/files/patch-doc_conf.py deleted file mode 100644 index a3ecb4c652db..000000000000 --- a/biology/py-orange3-single-cell/files/patch-doc_conf.py +++ /dev/null @@ -1,10 +0,0 @@ -# add_stylesheet() deprecated on Sphinx 4.0 -# https://www.sphinx-doc.org/en/master/extdev/deprecated.html ---- doc/conf.py.orig 2018-10-15 08:43:14 UTC -+++ doc/conf.py -@@ -288,4 +288,4 @@ texinfo_documents = [ - #texinfo_no_detailmenu = False - - def setup(app): -- app.add_stylesheet('style.css') -+ app.add_css_file('style.css') diff --git a/biology/py-orange3-single-cell/pkg-descr b/biology/py-orange3-single-cell/pkg-descr deleted file mode 100644 index 05cf4bfc5f8a..000000000000 --- a/biology/py-orange3-single-cell/pkg-descr +++ /dev/null @@ -1,2 +0,0 @@ -The Single Cell add-on for Orange3 adds functionality for analysis of single -cell data. diff --git a/biology/py-pydeseq2/Makefile b/biology/py-pydeseq2/Makefile new file mode 100644 index 000000000000..e31c4eb3d0ab --- /dev/null +++ b/biology/py-pydeseq2/Makefile @@ -0,0 +1,26 @@ +PORTNAME= pydeseq2 +DISTVERSION= 0.5.1 +CATEGORIES= biology python +MASTER_SITES= PYPI +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Python implementation of the popular DESeq2 R package +WWW= https://github.com/owkin/PyDESeq2 + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}anndata>=0.8.0:devel/py-anndata@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}formulaic>=1.0.2:math/py-formulaic@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}formulaic_contrasts>=0.2.0:math/py-formulaic-contrasts@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.6.2:math/py-matplotlib@${PY_FLAVOR} \ + ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}pandas>=1.4.0:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scikit-learn>=1.1.0:science/py-scikit-learn@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>1.11.0:science/py-scipy@${PY_FLAVOR} + +USES= python +USE_PYTHON= autoplist distutils + +.include <bsd.port.mk> diff --git a/biology/py-pydeseq2/distinfo b/biology/py-pydeseq2/distinfo new file mode 100644 index 000000000000..026ce31f8ca4 --- /dev/null +++ b/biology/py-pydeseq2/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1749586728 +SHA256 (pydeseq2-0.5.1.tar.gz) = 1ec79299f9134748b18bd8242ee4f7f6ccc9407dd18bf32562e051ae5cca626e +SIZE (pydeseq2-0.5.1.tar.gz) = 51390 diff --git a/biology/py-pydeseq2/pkg-descr b/biology/py-pydeseq2/pkg-descr new file mode 100644 index 000000000000..5f4c74926b39 --- /dev/null +++ b/biology/py-pydeseq2/pkg-descr @@ -0,0 +1,4 @@ +PyDESeq2 is a python implementation of the DESeq2 method for +differential expression analysis (DEA) with bulk RNA-seq data, +originally in R. It aims to facilitate DEA experiments for python +users. diff --git a/biology/py-pyrodigal/Makefile b/biology/py-pyrodigal/Makefile index d4dfc118e33b..631c485bdc47 100644 --- a/biology/py-pyrodigal/Makefile +++ b/biology/py-pyrodigal/Makefile @@ -24,7 +24,7 @@ xpost-build: @cd ${BUILD_WRKSRC} && ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py build_ext --inplace post-install: - @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pyrodigal/lib${PYTHON_EXT_SUFFIX}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pyrodigal/lib${PYTHON_TAG}.so do-test: # as of 3.6.3 this doesn't work: https://github.com/althonos/pyrodigal/issues/63 @cd ${TEST_WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -vv diff --git a/biology/py-pysam/Makefile b/biology/py-pysam/Makefile index 9d7b001423a0..d3cb9328b978 100644 --- a/biology/py-pysam/Makefile +++ b/biology/py-pysam/Makefile @@ -31,7 +31,7 @@ TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} TEST_WRKSRC= ${WRKSRC}/tests post-install: - @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysam/lib*${PYTHON_EXT_SUFFIX}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysam/lib*${PYTHON_TAG}.so # tests as of 0.23.0: 958 passed, 13 skipped, 1 warning in 502.60s (0:08:22) diff --git a/biology/py-python-libsbml/pkg-plist b/biology/py-python-libsbml/pkg-plist index 092f79185065..093d26c8435f 100644 --- a/biology/py-python-libsbml/pkg-plist +++ b/biology/py-python-libsbml/pkg-plist @@ -1,3 +1,3 @@ %%PYTHON_SITELIBDIR%%/libsbml/__init__.py -%%PYTHON_SITELIBDIR%%/libsbml/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc -%%PYTHON_SITELIBDIR%%/libsbml/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON_SITELIBDIR%%/libsbml/__pycache__/__init__%%PYTHON_TAG%%.opt-1.pyc +%%PYTHON_SITELIBDIR%%/libsbml/__pycache__/__init__%%PYTHON_TAG%%.pyc diff --git a/biology/py-scikit-bio/Makefile b/biology/py-scikit-bio/Makefile index 4297e08f2c1c..f3451e54a4bf 100644 --- a/biology/py-scikit-bio/Makefile +++ b/biology/py-scikit-bio/Makefile @@ -49,8 +49,8 @@ CXXFLAGS+= -msse2 post-install: @${STRIP_CMD} \ - ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*${PYTHON_EXT_SUFFIX}.so \ - ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*/*${PYTHON_EXT_SUFFIX}.so + ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*${PYTHON_TAG}.so \ + ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/skbio/*/*/*${PYTHON_TAG}.so do-test: # tests fail to run in a regular way, see https://github.com/biocore/scikit-bio/issues/1846 @cd ${STAGEDIR}${PYTHON_SITELIBDIR} && \ diff --git a/biology/salmon/Makefile b/biology/salmon/Makefile index 071e7fa2dc03..74631d470a17 100644 --- a/biology/salmon/Makefile +++ b/biology/salmon/Makefile @@ -1,7 +1,7 @@ PORTNAME= salmon DISTVERSIONPREFIX= v DISTVERSION= 1.10.2 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile index 496dfc8af2a1..f0ce1807eecd 100644 --- a/biology/samtools/Makefile +++ b/biology/samtools/Makefile @@ -1,5 +1,5 @@ PORTNAME= samtools -DISTVERSION= 1.21 +DISTVERSION= 1.22 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -9,7 +9,7 @@ WWW= https://www.htslib.org/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE -BUILD_DEPENDS= htslib>=1.21:biology/htslib +BUILD_DEPENDS= htslib>=1.22:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib TEST_DEPENDS= bash:shells/bash diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo index 867f9408bd11..69760896c894 100644 --- a/biology/samtools/distinfo +++ b/biology/samtools/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1727437810 -SHA256 (samtools-samtools-1.21_GH0.tar.gz) = b327b85d3d60771ede370c8bcae0570e7704da39abddfe8e930a85b80aabffac -SIZE (samtools-samtools-1.21_GH0.tar.gz) = 5682709 +TIMESTAMP = 1748951307 +SHA256 (samtools-samtools-1.22_GH0.tar.gz) = dbe62a97d19634a930033ce302b340a5109263efc371b83481182385a98bcdda +SIZE (samtools-samtools-1.22_GH0.tar.gz) = 5742299 diff --git a/biology/samtools/pkg-plist b/biology/samtools/pkg-plist index 2ef37918b44f..f841e6b58a07 100644 --- a/biology/samtools/pkg-plist +++ b/biology/samtools/pkg-plist @@ -26,6 +26,7 @@ share/man/man1/samtools-ampliconstats.1.gz share/man/man1/samtools-bedcov.1.gz share/man/man1/samtools-calmd.1.gz share/man/man1/samtools-cat.1.gz +share/man/man1/samtools-checksum.1.gz share/man/man1/samtools-collate.1.gz share/man/man1/samtools-consensus.1.gz share/man/man1/samtools-coverage.1.gz diff --git a/biology/seqkit/Makefile b/biology/seqkit/Makefile index 2d1577a4a940..e50fa5474365 100644 --- a/biology/seqkit/Makefile +++ b/biology/seqkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= seqkit DISTVERSIONPREFIX= v DISTVERSION= 2.10.0 -PORTREVISION= 1 +PORTREVISION= 3 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/seqtk/Makefile b/biology/seqtk/Makefile index 0a7e6ac9682b..cd861e2c4906 100644 --- a/biology/seqtk/Makefile +++ b/biology/seqtk/Makefile @@ -1,6 +1,6 @@ PORTNAME= seqtk DISTVERSIONPREFIX= v -DISTVERSION= 1.4 +DISTVERSION= 1.5 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -12,6 +12,7 @@ LICENSE= GPLv2 USE_GITHUB= yes GH_ACCOUNT= lh3 +INSTALL_TARGET= install-strip PLIST_FILES= bin/seqtk .include <bsd.port.mk> diff --git a/biology/seqtk/distinfo b/biology/seqtk/distinfo index b790163bdb01..40629eaef168 100644 --- a/biology/seqtk/distinfo +++ b/biology/seqtk/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1684848703 -SHA256 (lh3-seqtk-v1.4_GH0.tar.gz) = d124604ec24f29ed14ce127426ab90e0f3a2c0280c80d1a3ff8b1c09feede19c -SIZE (lh3-seqtk-v1.4_GH0.tar.gz) = 23748 +TIMESTAMP = 1748953617 +SHA256 (lh3-seqtk-v1.5_GH0.tar.gz) = 384aa1e3cecf4f70403839d586cbb29d469b7c6f773a64bc5af48a6e4b8220a6 +SIZE (lh3-seqtk-v1.5_GH0.tar.gz) = 24050 diff --git a/biology/seqtk/files/patch-Makefile b/biology/seqtk/files/patch-Makefile index ab373642a46e..d8acf547402e 100644 --- a/biology/seqtk/files/patch-Makefile +++ b/biology/seqtk/files/patch-Makefile @@ -1,34 +1,41 @@ ---- Makefile.orig 2018-06-18 00:15:09 UTC +--- Makefile.orig 2025-06-01 19:24:24 UTC +++ Makefile -@@ -1,14 +1,23 @@ +@@ -1,14 +1,30 @@ -CC=gcc --CFLAGS=-g -Wall -O2 -Wno-unused-function +-CFLAGS=-g -Wall -O2 -Wno-unused-function -Wno-format -BINDIR=/usr/local/bin - --all:seqtk +# Respect user's build environment by using ?= to set defaults for variables +# not set in the env or make arguments. Use += to add essential args. - --seqtk:seqtk.c khash.h kseq.h -- $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm ++ +CC ?= gcc -+CFLAGS ?= -g -Wall -O2 -Wno-unused-function ++CFLAGS ?= -g -Wall -O2 ++CFLAGS += -Wno-unused-function -Wno-format +LDFLAGS += -lz -lm +PREFIX ?= /usr/local ++STRIP ?= strip ++BINDIR= $(PREFIX)/bin + +-all:seqtk +MKDIR ?= mkdir +INSTALL ?= install -+# DESTDIR is empty by default to install straight to PREFIX --install:all -- install seqtk $(BINDIR) +-seqtk:seqtk.c khash.h kseq.h +- $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm +all: seqtk +-install:all +- install seqtk $(BINDIR) +seqtk: seqtk.c khash.h kseq.h + $(CC) $(CFLAGS) seqtk.c -o $@ $(LDFLAGS) -+ + ++# Add DESTDIR staged install support ++# DESTDIR is empty by default to install straight to PREFIX +install: all -+ $(MKDIR) -p $(DESTDIR)$(PREFIX)/bin -+ $(INSTALL) -c -m 0755 seqtk $(DESTDIR)$(PREFIX)/bin ++ $(MKDIR) -p $(DESTDIR)$(BINDIR) ++ $(INSTALL) -c -m 0755 seqtk $(DESTDIR)$(BINDIR) ++ ++install-strip: install ++ $(STRIP) $(DESTDIR)$(BINDIR)/seqtk + clean: - rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session* diff --git a/biology/taxonkit/Makefile b/biology/taxonkit/Makefile index dfe61730aaee..d245a195a8a5 100644 --- a/biology/taxonkit/Makefile +++ b/biology/taxonkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= taxonkit DISTVERSIONPREFIX= v DISTVERSION= 0.19.0 -PORTREVISION= 1 +PORTREVISION= 3 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/unikmer/Makefile b/biology/unikmer/Makefile index 364d635628d0..28443a6eb8f7 100644 --- a/biology/unikmer/Makefile +++ b/biology/unikmer/Makefile @@ -1,7 +1,7 @@ PORTNAME= unikmer DISTVERSIONPREFIX= v DISTVERSION= 0.20.0 -PORTREVISION= 5 +PORTREVISION= 7 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/vcflib/files/patch-src-zig-samples.zig b/biology/vcflib/files/patch-src-zig-samples.zig new file mode 100644 index 000000000000..e69584b175e0 --- /dev/null +++ b/biology/vcflib/files/patch-src-zig-samples.zig @@ -0,0 +1,31 @@ +diff --git src/zig/samples.zig src/zig/samples.zig +index cb05a1f2..ccd5b149 100644 +--- src/zig/samples.zig ++++ src/zig/samples.zig +@@ -28,7 +28,11 @@ const GENOTYPE_MISSING = -256; + fn split_samples(str: []const u8) *ArrayList([] const u8) { + var list = ArrayList([] const u8).init(allocator); + defer list.deinit(); +- var splits = std.mem.split(u8, str, " "); ++ ++ var splits = if (@hasDecl(std.mem, "splitScalar")) ++ std.mem.splitScalar(u8, str, ' ') ++ else ++ std.mem.split(u8, str, ' '); + while (splits.next()) |chunk| { + list.append(chunk) catch |err| { + std.debug.print("out of memory {}\n", .{err}); +@@ -61,10 +65,10 @@ const Genotypes = struct { + fn to_num(str: []const u8) !ArrayList(i64) { + var list = ArrayList(i64).init(allocator); + +- var splits = if (is_phased(str)) +- std.mem.split(u8, str, "|") ++ var splits = if (@hasDecl(std.mem, "splitScalar")) ++ std.mem.splitScalar(u8, str, if (is_phased(str)) '|' else '/') + else +- std.mem.split(u8, str, "/"); ++ std.mem.split(u8, str, if (is_phased(str)) '|' else '/' ); + + while (splits.next()) |chunk| { + const i: i64 = diff --git a/biology/vcflib/pkg-plist b/biology/vcflib/pkg-plist index d5e562de28bf..b50497d0c267 100644 --- a/biology/vcflib/pkg-plist +++ b/biology/vcflib/pkg-plist @@ -159,7 +159,7 @@ include/vcflib/var.hpp include/vcflib/vcf-c-api.h include/vcflib/vcf-wfa.h lib/libvcflib.a -lib/pyvcflib%%PYTHON_EXT_SUFFIX%%.so +lib/pyvcflib%%PYTHON_TAG%%.so share/man/man1/abba-baba.1.gz share/man/man1/bFst.1.gz share/man/man1/dumpContigsFromHeader.1.gz diff --git a/biology/vcftools/Makefile b/biology/vcftools/Makefile index e7d8ab338312..5c3b2d72c47b 100644 --- a/biology/vcftools/Makefile +++ b/biology/vcftools/Makefile @@ -1,7 +1,6 @@ PORTNAME= vcftools -PORTVERSION= 0.1.16 +PORTVERSION= 0.1.17 DISTVERSIONPREFIX= v -PORTREVISION= 2 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -11,11 +10,10 @@ WWW= https://github.com/vcftools/vcftools LICENSE= LGPL3 USES= autoreconf cpe gmake perl5 pkgconfig - -GNU_CONFIGURE= yes -GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share USE_GITHUB= yes +GNU_CONFIGURE= yes +GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share CXXFLAGS+= -std=c++14 CPE_VENDOR= vcftools_project diff --git a/biology/vcftools/distinfo b/biology/vcftools/distinfo index 14a425bfc4c0..5a5c2ff84384 100644 --- a/biology/vcftools/distinfo +++ b/biology/vcftools/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1533330712 -SHA256 (vcftools-vcftools-v0.1.16_GH0.tar.gz) = 575c13073efe65cbff6e2ab99eef12fe04536f5dc1f98de6674c848ca83cf302 -SIZE (vcftools-vcftools-v0.1.16_GH0.tar.gz) = 246933 +TIMESTAMP = 1747310968 +SHA256 (vcftools-vcftools-v0.1.17_GH0.tar.gz) = 00b54fc7349179c2efbdab0e4dcb65a69e7b0ab0d0d29b59cc823140d0b40bff +SIZE (vcftools-vcftools-v0.1.17_GH0.tar.gz) = 247685 |