diff options
Diffstat (limited to 'biology')
44 files changed, 108 insertions, 800 deletions
diff --git a/biology/Makefile b/biology/Makefile index 742a6885b0d2..2a6da67d4b30 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -142,7 +142,6 @@ SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam - SUBDIR += pbseqan SUBDIR += peak-classifier SUBDIR += pear-merger SUBDIR += phrap diff --git a/biology/R-cran-BiocManager/Makefile b/biology/R-cran-BiocManager/Makefile index 2ecab572d8e4..1e183d284ef1 100644 --- a/biology/R-cran-BiocManager/Makefile +++ b/biology/R-cran-BiocManager/Makefile @@ -1,5 +1,5 @@ PORTNAME= BiocManager -PORTVERSION= 1.30.22 +DISTVERSION= 1.30.23 CATEGORIES= biology DISTNAME= ${PORTNAME}_${PORTVERSION} diff --git a/biology/R-cran-BiocManager/distinfo b/biology/R-cran-BiocManager/distinfo index e007f57ce45d..e1187c698077 100644 --- a/biology/R-cran-BiocManager/distinfo +++ b/biology/R-cran-BiocManager/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1702634634 -SHA256 (BiocManager_1.30.22.tar.gz) = 5389c9c0d6562b0757659fb8262ab51b48225c4ba7e9acd4f5e7c0049735e835 -SIZE (BiocManager_1.30.22.tar.gz) = 582690 +TIMESTAMP = 1715459288 +SHA256 (BiocManager_1.30.23.tar.gz) = f7b45dbc49c97b2e6ec4b96ec1d472c6f1a5ad9bc0f933eea4c3ebc90dd8f34c +SIZE (BiocManager_1.30.23.tar.gz) = 589753 diff --git a/biology/ad2vcf/Makefile b/biology/ad2vcf/Makefile index 6c1edd2e4dc3..deb77422ba42 100644 --- a/biology/ad2vcf/Makefile +++ b/biology/ad2vcf/Makefile @@ -1,6 +1,6 @@ PORTNAME= ad2vcf -DISTVERSION= 0.1.6 -PORTREVISION= 1 +DISTVERSION= 0.1.6-19 +DISTVERSIONSUFFIX= -gf42ae91 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/ad2vcf/distinfo b/biology/ad2vcf/distinfo index 316c31f1b437..8af7ae6d8682 100644 --- a/biology/ad2vcf/distinfo +++ b/biology/ad2vcf/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1654951938 -SHA256 (auerlab-ad2vcf-0.1.6_GH0.tar.gz) = fbed1e32504dbc6975cb124792d12e48576ed799ac148aa3b6beed33a67bdf98 -SIZE (auerlab-ad2vcf-0.1.6_GH0.tar.gz) = 16293 +TIMESTAMP = 1716122785 +SHA256 (auerlab-ad2vcf-0.1.6-19-gf42ae91_GH0.tar.gz) = d71a584e8b74e853a8595ddfa7327959b2fc991b5c6034e9402024384e7a1297 +SIZE (auerlab-ad2vcf-0.1.6-19-gf42ae91_GH0.tar.gz) = 16176 diff --git a/biology/augustus/Makefile b/biology/augustus/Makefile index f5725eb93f47..1694ab2bd5aa 100644 --- a/biology/augustus/Makefile +++ b/biology/augustus/Makefile @@ -1,7 +1,7 @@ PORTNAME= augustus DISTVERSIONPREFIX= v DISTVERSION= 3.5.0 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= biology science PKGNAMESUFFIX= -gene-prediction diff --git a/biology/biolibc/Makefile b/biology/biolibc/Makefile index 954784150868..fd2e2a4b4e85 100644 --- a/biology/biolibc/Makefile +++ b/biology/biolibc/Makefile @@ -1,6 +1,6 @@ PORTNAME= biolibc -DISTVERSION= 0.2.6 -PORTREVISION= 1 +DISTVERSION= 0.2.6-4 +DISTVERSIONSUFFIX= -g723ac84 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/biolibc/distinfo b/biology/biolibc/distinfo index 5cf48814bfd6..8381fe58abcf 100644 --- a/biology/biolibc/distinfo +++ b/biology/biolibc/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1698064273 -SHA256 (auerlab-biolibc-0.2.6_GH0.tar.gz) = d3807734b6e615e7655d86591778784f8360fc30c37a0beff54212193d3c3dd0 -SIZE (auerlab-biolibc-0.2.6_GH0.tar.gz) = 147823 +TIMESTAMP = 1716122167 +SHA256 (auerlab-biolibc-0.2.6-4-g723ac84_GH0.tar.gz) = d467c954b3d7ffaafe1dea36006113bf7b412285fdc07e71c504fd5b5db5ae64 +SIZE (auerlab-biolibc-0.2.6-4-g723ac84_GH0.tar.gz) = 147951 diff --git a/biology/biosig/Makefile b/biology/biosig/Makefile index f34dfee41237..5e1d2b6e50c7 100644 --- a/biology/biosig/Makefile +++ b/biology/biosig/Makefile @@ -1,5 +1,6 @@ PORTNAME= biosig DISTVERSION= 2.6.0 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= SF/${PORTNAME}/BioSig%20for%20C_C%2B%2B/src/ DISTNAME= ${PORTNAME}-${PORTVERSION}.src diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile index 97bceda17ba2..2bd78e1e9925 100644 --- a/biology/hyphy/Makefile +++ b/biology/hyphy/Makefile @@ -1,5 +1,5 @@ PORTNAME= hyphy -DISTVERSION= 2.5.60 +DISTVERSION= 2.5.61 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo index ebff1227db85..2129a0dda3e7 100644 --- a/biology/hyphy/distinfo +++ b/biology/hyphy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1713128763 -SHA256 (veg-hyphy-2.5.60_GH0.tar.gz) = bc3a5062ee3cee47de16c394189fb8a5feed48f9a8c12302432d6faa7f2ac301 -SIZE (veg-hyphy-2.5.60_GH0.tar.gz) = 5599910 +TIMESTAMP = 1715871637 +SHA256 (veg-hyphy-2.5.61_GH0.tar.gz) = 5a470ad64e9ea53296d87e69298ab2354d563338a9ec05b529679c42e23b3025 +SIZE (veg-hyphy-2.5.61_GH0.tar.gz) = 5604227 diff --git a/biology/iqtree/Makefile b/biology/iqtree/Makefile index 5752c102500c..fc48fb410933 100644 --- a/biology/iqtree/Makefile +++ b/biology/iqtree/Makefile @@ -1,6 +1,6 @@ PORTNAME= iqtree -DISTVERSIONPREFIX= v -DISTVERSION= 2.3.2 +DISTVERSIONPREFIX= v. +DISTVERSION= 2.3.4 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org diff --git a/biology/iqtree/distinfo b/biology/iqtree/distinfo index 4b5ff2269f5f..ebd56f55dff4 100644 --- a/biology/iqtree/distinfo +++ b/biology/iqtree/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1713099860 -SHA256 (iqtree-iqtree2-v2.3.2_GH0.tar.gz) = c1f97b5fba459561739f4213e7014f29049e070f0cbe2a20473279b372e3c12e -SIZE (iqtree-iqtree2-v2.3.2_GH0.tar.gz) = 6161544 +TIMESTAMP = 1715872647 +SHA256 (iqtree-iqtree2-v.2.3.4_GH0.tar.gz) = 35bdac31c5795e5c72e532c2a311aa8266c9d40e7d668ee84c3b6e975af318da +SIZE (iqtree-iqtree2-v.2.3.4_GH0.tar.gz) = 6568572 SHA256 (tothuhien-lsd2-26ba127_GH0.tar.gz) = 63226da0e326d9fc47c54e8e380d48e51e923ccc25bd7f286d49b9f49028d1c4 SIZE (tothuhien-lsd2-26ba127_GH0.tar.gz) = 1079490 diff --git a/biology/iqtree/files/patch-CMakeLists.txt b/biology/iqtree/files/patch-CMakeLists.txt deleted file mode 100644 index d52f30670d91..000000000000 --- a/biology/iqtree/files/patch-CMakeLists.txt +++ /dev/null @@ -1,11 +0,0 @@ ---- CMakeLists.txt.orig 2023-09-05 01:20:58 UTC -+++ CMakeLists.txt -@@ -398,7 +398,7 @@ if (NOT IQTREE_FLAGS MATCHES "single") - else() - link_directories(${PROJECT_SOURCE_DIR}/libmac) - endif() -- elseif (WIN32 OR UNIX) -+ elseif (WIN32 OR UNIX AND NOT ${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD") - if (BINARY32) - link_directories(${PROJECT_SOURCE_DIR}/lib32) - else() diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index 8774208d9097..158ff03a9137 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -1,6 +1,7 @@ PORTNAME= kallisto DISTVERSIONPREFIX= v DISTVERSION= 0.50.1 +PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= biology @@ -22,6 +23,8 @@ USES= cmake:noninja compiler:c++11-lang gmake localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= pachterlab +EXTRACT_AFTER_ARGS= --exclude ${GH_PROJECT_DEFAULT}-${GH_TAGNAME_EXTRACT}/ext/htslib --no-same-owner --no-same-permissions + SUB_FILES= kallisto-test PORTEXAMPLES= * @@ -39,9 +42,6 @@ LDFLAGS+= -lhts -lz OPTIONS_DEFINE= EXAMPLES -post-extract: - ${RM} -rf ${WRKSRC}/ext/htslib - post-install-EXAMPLES-on: ${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} diff --git a/biology/kmcp/Makefile b/biology/kmcp/Makefile index 766256b0ce9c..7759581a8279 100644 --- a/biology/kmcp/Makefile +++ b/biology/kmcp/Makefile @@ -1,7 +1,7 @@ PORTNAME= kmcp DISTVERSIONPREFIX= v DISTVERSION= 0.9.4 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/mothur/Makefile b/biology/mothur/Makefile index 695bcdc7fefc..6c7d3f28d684 100644 --- a/biology/mothur/Makefile +++ b/biology/mothur/Makefile @@ -1,6 +1,6 @@ PORTNAME= mothur DISTVERSIONPREFIX= v -DISTVERSION= 1.48.0 +DISTVERSION= 1.48.1 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/mothur/distinfo b/biology/mothur/distinfo index 075596197498..b54fca86abc6 100644 --- a/biology/mothur/distinfo +++ b/biology/mothur/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1652984425 -SHA256 (mothur-mothur-v1.48.0_GH0.tar.gz) = 9494406abd8d14b821782ab9db811f045ded9424f28f01234ee6764d4e78941d -SIZE (mothur-mothur-v1.48.0_GH0.tar.gz) = 1652711 +TIMESTAMP = 1715831777 +SHA256 (mothur-mothur-v1.48.1_GH0.tar.gz) = 03a26d12719b8658051b0c2aefe791017d9bdcc6d50ba539f85ed232daafc0ac +SIZE (mothur-mothur-v1.48.1_GH0.tar.gz) = 1654064 diff --git a/biology/ncbi-cxx-toolkit/Makefile b/biology/ncbi-cxx-toolkit/Makefile index fb7fff520847..86f50ccfbd47 100644 --- a/biology/ncbi-cxx-toolkit/Makefile +++ b/biology/ncbi-cxx-toolkit/Makefile @@ -1,7 +1,6 @@ PORTNAME= ncbi-cxx-toolkit DISTVERSIONPREFIX= release- -DISTVERSION= 28.0.3 -PORTREVISION= 1 +DISTVERSION= 28.0.4 CATEGORIES= biology science devel MAINTAINER= yuri@FreeBSD.org diff --git a/biology/ncbi-cxx-toolkit/distinfo b/biology/ncbi-cxx-toolkit/distinfo index bbf6b145974a..a76dc55206bc 100644 --- a/biology/ncbi-cxx-toolkit/distinfo +++ b/biology/ncbi-cxx-toolkit/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1712138582 -SHA256 (ncbi-ncbi-cxx-toolkit-public-release-28.0.3_GH0.tar.gz) = 070ba25981a77b9fd1bdb261c3f51f7819ea73dca99fa77a9ef806e252ab4367 -SIZE (ncbi-ncbi-cxx-toolkit-public-release-28.0.3_GH0.tar.gz) = 57037085 +TIMESTAMP = 1715055866 +SHA256 (ncbi-ncbi-cxx-toolkit-public-release-28.0.4_GH0.tar.gz) = 2e4583e7dcb22415633fc5329b0ddca15367d5db79a25d04303e295340441505 +SIZE (ncbi-ncbi-cxx-toolkit-public-release-28.0.4_GH0.tar.gz) = 57046657 diff --git a/biology/ncbi-entrez-direct/Makefile b/biology/ncbi-entrez-direct/Makefile index 933fd7d55791..772852564535 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= 20 +PORTREVISION= 21 CATEGORIES= biology perl5 MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/${PORTVERSION}/ DISTFILES= edirect.tar.gz diff --git a/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl b/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl index 5fc8fb532a2c..3d4ce73cdafd 100644 --- a/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl +++ b/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl @@ -1,6 +1,9 @@ ---- ngs-sdk/setup/konfigure.perl.orig 2021-08-18 16:26:23 UTC +- patch includes removal of '-arch i386' trying to fix build on i386: +- see https://github.com/ncbi/ngs/issues/39 + +--- ngs-sdk/setup/konfigure.perl.orig 2022-11-15 17:37:36 UTC +++ ngs-sdk/setup/konfigure.perl -@@ -225,7 +225,7 @@ if ($OS eq 'linux') { +@@ -225,7 +225,7 @@ println $MARCH unless ($AUTORUN); print "checking machine architecture... " unless ($AUTORUN); println $MARCH unless ($AUTORUN); @@ -9,7 +12,7 @@ println "configure: error: unsupported architecture '$OSTYPE':'$MARCH'"; exit 1; } -@@ -312,6 +312,8 @@ my $BITS; +@@ -312,6 +312,8 @@ if ($MARCH =~ /x86_64/i) { if ($MARCH =~ /x86_64/i) { $BITS = 64; @@ -35,3 +38,20 @@ } elsif ($OSTYPE =~ /darwin/i) { $LPFX = 'lib'; $OBJX = 'o'; +@@ -386,14 +398,14 @@ if ($TOOLS =~ /gcc$/) { + my $versionMin = '-mmacosx-version-min=10.10'; + $CP = "$CPP -c $versionMin"; + if ($BITS ne '32_64') { +- $ARCH_FL = '-arch i386' if ($BITS == 32); ++ $ARCH_FL = '' if ($BITS == 32); + $OPT = '-O3'; + $AR = 'ar rc'; + $LD = "clang $ARCH_FL"; + $LP = "$CPP $versionMin $ARCH_FL"; + } else { + $MAKE_MANIFEST = '( echo "$^" > $@/manifest )'; +- $ARCH_FL = '-arch i386 -arch x86_64'; ++ $ARCH_FL = '-arch x86_64'; + $OPT = '-O3'; + $AR = 'libtool -static -o'; + $LD = "clang -Wl,-arch_multiple $ARCH_FL -Wl,-all_load"; diff --git a/biology/pbseqan/Makefile b/biology/pbseqan/Makefile deleted file mode 100644 index a7d8d6e04759..000000000000 --- a/biology/pbseqan/Makefile +++ /dev/null @@ -1,30 +0,0 @@ -PORTNAME= pbseqan -DISTVERSION= g20171011 -CATEGORIES= biology - -# As of March 2018, unanimity is no longer open source. -# See https://github.com/PacificBiosciences/ccs. -MAINTAINER= ports@FreeBSD.org -COMMENT= Pacific Biosciences patched and stripped down SeqAn -WWW= https://github.com/PacificBiosciences/seqan - -LICENSE= BSD3CLAUSE -LICENSE_FILE= ${WRKSRC}/LICENSE - -DEPRECATED= Upstream merged into SeqAn project: Use biology/seqan -EXPIRATION_DATE= 2024-05-05 - -USE_GITHUB= yes -GH_ACCOUNT= PacificBiosciences -GH_PROJECT= seqan -GH_TAGNAME= 21d95d737d8decb5cc3693b9065d81e831e7f57d - -NO_BUILD= yes -NO_ARCH= yes - -do-install: - @${MKDIR} ${STAGEDIR}${PREFIX}/include/PacBio - cd ${WRKSRC}/include/seqan && \ - ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include/PacBio/seqan - -.include <bsd.port.mk> diff --git a/biology/pbseqan/distinfo b/biology/pbseqan/distinfo deleted file mode 100644 index ac3b9e5292f5..000000000000 --- a/biology/pbseqan/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1550366556 -SHA256 (PacificBiosciences-seqan-g20171011-21d95d737d8decb5cc3693b9065d81e831e7f57d_GH0.tar.gz) = dcdc564c877190089bd691ab4097164266e675217645613426fb1ff44029da8c -SIZE (PacificBiosciences-seqan-g20171011-21d95d737d8decb5cc3693b9065d81e831e7f57d_GH0.tar.gz) = 1527033 diff --git a/biology/pbseqan/pkg-descr b/biology/pbseqan/pkg-descr deleted file mode 100644 index 40bf624533db..000000000000 --- a/biology/pbseqan/pkg-descr +++ /dev/null @@ -1,9 +0,0 @@ -This is a public fork of the SeqAn Library v2.0.0, stripped down to just the -header files and with a few custom fixes. - -Some of PacBio's tools depend on SeqAn for efficient implementations of some -common data-structures for sequence analysis (A huge thanks to SeqAn -development team!). However PacBio only uses a small amount of the SeqAn -code-base, and in addition requires a few minor fixes that didn't make it in to -the initial release of SeqAn v2.0.0. Thus to minimize confusion and band-width, -we will depend on this fork instead of SeqAn proper. diff --git a/biology/pbseqan/pkg-plist b/biology/pbseqan/pkg-plist deleted file mode 100644 index a5019b19b101..000000000000 --- a/biology/pbseqan/pkg-plist +++ /dev/null @@ -1,657 +0,0 @@ -include/PacBio/seqan/LICENSE -include/PacBio/seqan/align.h -include/PacBio/seqan/align/align_base.h -include/PacBio/seqan/align/align_cols.h -include/PacBio/seqan/align/align_config.h -include/PacBio/seqan/align/align_iterator_base.h -include/PacBio/seqan/align/align_metafunctions.h -include/PacBio/seqan/align/align_traceback.h -include/PacBio/seqan/align/alignment_algorithm_tags.h -include/PacBio/seqan/align/alignment_operations.h -include/PacBio/seqan/align/dp_algorithm_impl.h -include/PacBio/seqan/align/dp_band.h -include/PacBio/seqan/align/dp_cell.h -include/PacBio/seqan/align/dp_cell_affine.h -include/PacBio/seqan/align/dp_cell_dynamic.h -include/PacBio/seqan/align/dp_cell_linear.h -include/PacBio/seqan/align/dp_context.h -include/PacBio/seqan/align/dp_formula.h -include/PacBio/seqan/align/dp_formula_affine.h -include/PacBio/seqan/align/dp_formula_dynamic.h -include/PacBio/seqan/align/dp_formula_linear.h -include/PacBio/seqan/align/dp_matrix.h -include/PacBio/seqan/align/dp_matrix_navigator.h -include/PacBio/seqan/align/dp_matrix_navigator_score_matrix.h -include/PacBio/seqan/align/dp_matrix_navigator_score_matrix_sparse.h -include/PacBio/seqan/align/dp_matrix_navigator_trace_matrix.h -include/PacBio/seqan/align/dp_matrix_sparse.h -include/PacBio/seqan/align/dp_meta_info.h -include/PacBio/seqan/align/dp_profile.h -include/PacBio/seqan/align/dp_scout.h -include/PacBio/seqan/align/dp_setup.h -include/PacBio/seqan/align/dp_trace_segment.h -include/PacBio/seqan/align/dp_traceback_adaptor.h -include/PacBio/seqan/align/dp_traceback_impl.h -include/PacBio/seqan/align/evaluate_alignment.h -include/PacBio/seqan/align/fragment.h -include/PacBio/seqan/align/gap_anchor.h -include/PacBio/seqan/align/gapped_value_type.h -include/PacBio/seqan/align/gaps_anchor.h -include/PacBio/seqan/align/gaps_array.h -include/PacBio/seqan/align/gaps_base.h -include/PacBio/seqan/align/gaps_iterator_anchor.h -include/PacBio/seqan/align/gaps_iterator_array.h -include/PacBio/seqan/align/gaps_iterator_base.h -include/PacBio/seqan/align/global_alignment_banded.h -include/PacBio/seqan/align/global_alignment_hirschberg_impl.h -include/PacBio/seqan/align/global_alignment_myers_hirschberg_impl.h -include/PacBio/seqan/align/global_alignment_myers_impl.h -include/PacBio/seqan/align/global_alignment_specialized.h -include/PacBio/seqan/align/global_alignment_unbanded.h -include/PacBio/seqan/align/local_alignment_banded.h -include/PacBio/seqan/align/local_alignment_banded_waterman_eggert_impl.h -include/PacBio/seqan/align/local_alignment_enumeration.h -include/PacBio/seqan/align/local_alignment_enumeration_banded.h -include/PacBio/seqan/align/local_alignment_enumeration_unbanded.h -include/PacBio/seqan/align/local_alignment_unbanded.h -include/PacBio/seqan/align/local_alignment_waterman_eggert_impl.h -include/PacBio/seqan/align/matrix_base.h -include/PacBio/seqan/align_extend.h -include/PacBio/seqan/align_extend/align_extend.h -include/PacBio/seqan/align_extend/align_extend_base.h -include/PacBio/seqan/align_extend/dp_scout_xdrop.h -include/PacBio/seqan/align_profile.h -include/PacBio/seqan/align_profile/add_to_profile.h -include/PacBio/seqan/align_profile/score_profile_seq.h -include/PacBio/seqan/align_split.h -include/PacBio/seqan/align_split/align_split_interface.h -include/PacBio/seqan/align_split/dp_scout_split.h -include/PacBio/seqan/alignment_free.h -include/PacBio/seqan/alignment_free/af_d2.h -include/PacBio/seqan/alignment_free/af_d2star.h -include/PacBio/seqan/alignment_free/af_d2z.h -include/PacBio/seqan/alignment_free/af_n2.h -include/PacBio/seqan/alignment_free/alignment_free_base.h -include/PacBio/seqan/alignment_free/alignment_free_comparison.h -include/PacBio/seqan/alignment_free/kmer_functions.h -include/PacBio/seqan/arg_parse.h -include/PacBio/seqan/arg_parse/arg_parse_argument.h -include/PacBio/seqan/arg_parse/arg_parse_ctd_support.h -include/PacBio/seqan/arg_parse/arg_parse_doc.h -include/PacBio/seqan/arg_parse/arg_parse_exceptions.h -include/PacBio/seqan/arg_parse/arg_parse_option.h -include/PacBio/seqan/arg_parse/arg_parse_parse.h -include/PacBio/seqan/arg_parse/arg_parse_type_support.h -include/PacBio/seqan/arg_parse/argument_parser.h -include/PacBio/seqan/arg_parse/tool_doc.h -include/PacBio/seqan/arg_parse/xml_support.h -include/PacBio/seqan/bam_io.h -include/PacBio/seqan/bam_io/bam_alignment_record.h -include/PacBio/seqan/bam_io/bam_alignment_record_util.h -include/PacBio/seqan/bam_io/bam_file.h -include/PacBio/seqan/bam_io/bam_header_record.h -include/PacBio/seqan/bam_io/bam_index_bai.h -include/PacBio/seqan/bam_io/bam_io_context.h -include/PacBio/seqan/bam_io/bam_sam_conversion.h -include/PacBio/seqan/bam_io/bam_scanner_cache.h -include/PacBio/seqan/bam_io/bam_tags_dict.h -include/PacBio/seqan/bam_io/cigar.h -include/PacBio/seqan/bam_io/read_bam.h -include/PacBio/seqan/bam_io/read_sam.h -include/PacBio/seqan/bam_io/write_bam.h -include/PacBio/seqan/bam_io/write_sam.h -include/PacBio/seqan/basic.h -include/PacBio/seqan/basic/aggregate_concept.h -include/PacBio/seqan/basic/allocator_chunkpool.h -include/PacBio/seqan/basic/allocator_interface.h -include/PacBio/seqan/basic/allocator_multipool.h -include/PacBio/seqan/basic/allocator_simple.h -include/PacBio/seqan/basic/allocator_singlepool.h -include/PacBio/seqan/basic/allocator_to_std.h -include/PacBio/seqan/basic/alphabet_adapt_builtins.h -include/PacBio/seqan/basic/alphabet_bio.h -include/PacBio/seqan/basic/alphabet_concept.h -include/PacBio/seqan/basic/alphabet_math.h -include/PacBio/seqan/basic/alphabet_profile.h -include/PacBio/seqan/basic/alphabet_qualities.h -include/PacBio/seqan/basic/alphabet_residue.h 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-include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_base_late.h -include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h -include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h -include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h -include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h -include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h -include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h -include/PacBio/seqan/roi_io.h -include/PacBio/seqan/roi_io/read_roi.h -include/PacBio/seqan/roi_io/roi_file.h -include/PacBio/seqan/roi_io/roi_io_context.h -include/PacBio/seqan/roi_io/roi_record.h -include/PacBio/seqan/roi_io/write_roi.h -include/PacBio/seqan/score.h -include/PacBio/seqan/score/score_base.h -include/PacBio/seqan/score/score_edit.h -include/PacBio/seqan/score/score_matrix.h -include/PacBio/seqan/score/score_matrix_data.h -include/PacBio/seqan/score/score_matrix_io.h -include/PacBio/seqan/score/score_simple.h -include/PacBio/seqan/seeds.h -include/PacBio/seqan/seeds/banded_chain_alignment.h -include/PacBio/seqan/seeds/banded_chain_alignment_impl.h -include/PacBio/seqan/seeds/banded_chain_alignment_profile.h -include/PacBio/seqan/seeds/banded_chain_alignment_scout.h -include/PacBio/seqan/seeds/banded_chain_alignment_traceback.h -include/PacBio/seqan/seeds/basic_iter_indirect.h -include/PacBio/seqan/seeds/seeds_base.h -include/PacBio/seqan/seeds/seeds_combination.h -include/PacBio/seqan/seeds/seeds_extension.h -include/PacBio/seqan/seeds/seeds_global_chaining.h -include/PacBio/seqan/seeds/seeds_global_chaining_base.h -include/PacBio/seqan/seeds/seeds_global_chaining_gusfield.h -include/PacBio/seqan/seeds/seeds_seed_base.h -include/PacBio/seqan/seeds/seeds_seed_chained.h -include/PacBio/seqan/seeds/seeds_seed_diagonal.h -include/PacBio/seqan/seeds/seeds_seed_set_base.h -include/PacBio/seqan/seeds/seeds_seed_set_non_scored.h -include/PacBio/seqan/seeds/seeds_seed_set_scored.h -include/PacBio/seqan/seeds/seeds_seed_set_unordered.h -include/PacBio/seqan/seeds/seeds_seed_simple.h -include/PacBio/seqan/seq_io.h -include/PacBio/seqan/seq_io/fai_index.h -include/PacBio/seqan/seq_io/fasta_fastq.h -include/PacBio/seqan/seq_io/genomic_region.h -include/PacBio/seqan/seq_io/read_embl.h -include/PacBio/seqan/seq_io/read_genbank.h -include/PacBio/seqan/seq_io/sequence_file.h -include/PacBio/seqan/sequence.h -include/PacBio/seqan/sequence/adapt_array_pointer.h -include/PacBio/seqan/sequence/adapt_std_list.h -include/PacBio/seqan/sequence/adapt_std_string.h -include/PacBio/seqan/sequence/adapt_std_vector.h -include/PacBio/seqan/sequence/adapt_thrust_vector.h -include/PacBio/seqan/sequence/container_view.h -include/PacBio/seqan/sequence/iter_concat_virtual.h -include/PacBio/seqan/sequence/segment_base.h -include/PacBio/seqan/sequence/segment_infix.h -include/PacBio/seqan/sequence/segment_prefix.h -include/PacBio/seqan/sequence/segment_suffix.h -include/PacBio/seqan/sequence/segment_utils.h -include/PacBio/seqan/sequence/sequence_concatenator.h -include/PacBio/seqan/sequence/sequence_forwards.h -include/PacBio/seqan/sequence/sequence_interface.h -include/PacBio/seqan/sequence/sequence_lexical.h -include/PacBio/seqan/sequence/sequence_shortcuts.h -include/PacBio/seqan/sequence/string_alloc.h -include/PacBio/seqan/sequence/string_array.h -include/PacBio/seqan/sequence/string_base.h -include/PacBio/seqan/sequence/string_block.h -include/PacBio/seqan/sequence/string_cstyle.h -include/PacBio/seqan/sequence/string_packed.h -include/PacBio/seqan/sequence/string_packed_old.h -include/PacBio/seqan/sequence/string_set_base.h -include/PacBio/seqan/sequence/string_set_concat_direct.h -include/PacBio/seqan/sequence/string_set_dependent_generous.h -include/PacBio/seqan/sequence/string_set_dependent_tight.h -include/PacBio/seqan/sequence/string_set_device.h -include/PacBio/seqan/sequence/string_set_owner.h -include/PacBio/seqan/sequence/string_set_segment.h -include/PacBio/seqan/sequence/string_set_view.h -include/PacBio/seqan/sequence_journaled.h -include/PacBio/seqan/sequence_journaled/journal_entries_sorted_array.h -include/PacBio/seqan/sequence_journaled/journal_entry.h -include/PacBio/seqan/sequence_journaled/sequence_journaled.h -include/PacBio/seqan/sequence_journaled/sequence_journaled_iterator.h -include/PacBio/seqan/sequence_journaled/sequence_journaled_iterator_fast.h -include/PacBio/seqan/simple_intervals_io.h -include/PacBio/seqan/simple_intervals_io/simple_intervals_file.h -include/PacBio/seqan/simple_intervals_io/simple_intervals_io.h -include/PacBio/seqan/statistics.h -include/PacBio/seqan/statistics/statistics_base.h -include/PacBio/seqan/statistics/statistics_markov_model.h -include/PacBio/seqan/store.h -include/PacBio/seqan/store/store_align.h -include/PacBio/seqan/store/store_align_intervals.h -include/PacBio/seqan/store/store_all.h -include/PacBio/seqan/store/store_annotation.h -include/PacBio/seqan/store/store_base.h -include/PacBio/seqan/store/store_contig.h -include/PacBio/seqan/store/store_intervaltree.h -include/PacBio/seqan/store/store_io.h -include/PacBio/seqan/store/store_io_gff.h -include/PacBio/seqan/store/store_io_sam.h -include/PacBio/seqan/store/store_io_ucsc.h -include/PacBio/seqan/store/store_library.h -include/PacBio/seqan/store/store_matepair.h -include/PacBio/seqan/store/store_read.h -include/PacBio/seqan/stream.h -include/PacBio/seqan/stream/adapt_ios.h -include/PacBio/seqan/stream/buffered_stream.h -include/PacBio/seqan/stream/file_stream.h -include/PacBio/seqan/stream/formatted_file.h -include/PacBio/seqan/stream/guess_format.h -include/PacBio/seqan/stream/iostream_bgzf.h -include/PacBio/seqan/stream/iostream_bgzf_impl.h -include/PacBio/seqan/stream/iostream_bzip2.h -include/PacBio/seqan/stream/iostream_bzip2_impl.h -include/PacBio/seqan/stream/iostream_zip.h -include/PacBio/seqan/stream/iostream_zip_impl.h -include/PacBio/seqan/stream/iostream_zutil.h -include/PacBio/seqan/stream/iter_stream.h -include/PacBio/seqan/stream/lexical_cast.h -include/PacBio/seqan/stream/stream_base.h -include/PacBio/seqan/stream/stream_compressor.h -include/PacBio/seqan/stream/tokenization.h -include/PacBio/seqan/stream/virtual_stream.h -include/PacBio/seqan/system.h -include/PacBio/seqan/system/file_async.h -include/PacBio/seqan/system/file_directory.h -include/PacBio/seqan/system/file_forwards.h -include/PacBio/seqan/system/file_sync.h -include/PacBio/seqan/system/system_base.h -include/PacBio/seqan/system/system_condition.h -include/PacBio/seqan/system/system_critical_section.h -include/PacBio/seqan/system/system_event.h -include/PacBio/seqan/system/system_forwards.h -include/PacBio/seqan/system/system_mutex.h -include/PacBio/seqan/system/system_thread.h -include/PacBio/seqan/translation.h -include/PacBio/seqan/translation/translation.h -include/PacBio/seqan/translation/translation_tables.h -include/PacBio/seqan/ucsc_io.h -include/PacBio/seqan/ucsc_io/ucsc_file.h -include/PacBio/seqan/ucsc_io/ucsc_io.h -include/PacBio/seqan/ucsc_io/ucsc_record.h -include/PacBio/seqan/vcf_io.h -include/PacBio/seqan/vcf_io/read_vcf.h -include/PacBio/seqan/vcf_io/vcf_file.h -include/PacBio/seqan/vcf_io/vcf_header.h -include/PacBio/seqan/vcf_io/vcf_header_record.h -include/PacBio/seqan/vcf_io/vcf_io_context.h -include/PacBio/seqan/vcf_io/vcf_record.h -include/PacBio/seqan/vcf_io/write_vcf.h -include/PacBio/seqan/version.h diff --git a/biology/prodigy-lig/Makefile b/biology/prodigy-lig/Makefile index 220bf77a33c7..c6a6a72badf5 100644 --- a/biology/prodigy-lig/Makefile +++ b/biology/prodigy-lig/Makefile @@ -1,6 +1,6 @@ PORTNAME= prodigy-lig DISTVERSIONPREFIX= v -DISTVERSION= 1.1.0 +DISTVERSION= 1.1.1 CATEGORIES= biology python MAINTAINER= yuri@FreeBSD.org @@ -11,10 +11,11 @@ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}biopython>0:biology/py-biopython@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}biopython>0:biology/py-biopython@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}poetry-core>0:devel/py-poetry-core@${PY_FLAVOR} USES= gmake python -USE_PYTHON= distutils noflavors autoplist +USE_PYTHON= pep517 noflavors autoplist USE_GITHUB= yes GH_ACCOUNT= haddocking diff --git a/biology/prodigy-lig/distinfo b/biology/prodigy-lig/distinfo index a934c718530b..fb14a3af4599 100644 --- a/biology/prodigy-lig/distinfo +++ b/biology/prodigy-lig/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1711007516 -SHA256 (haddocking-prodigy-lig-v1.1.0_GH0.tar.gz) = 66991015aff86fee6f5cbbc7c28107843083223d3d1aa18b67a658f2bd54bcd4 -SIZE (haddocking-prodigy-lig-v1.1.0_GH0.tar.gz) = 156624 +TIMESTAMP = 1714194540 +SHA256 (haddocking-prodigy-lig-v1.1.1_GH0.tar.gz) = 22a6ed0cbec84dcc2d0f8b0bc8206c2e6c14a057307486648fc0919d9eca63ab +SIZE (haddocking-prodigy-lig-v1.1.1_GH0.tar.gz) = 156208 diff --git a/biology/protomol/Makefile b/biology/protomol/Makefile index 2cf78f936b13..f7084de677a1 100644 --- a/biology/protomol/Makefile +++ b/biology/protomol/Makefile @@ -1,6 +1,6 @@ PORTNAME= protomol PORTVERSION= 2.0.3 -PORTREVISION= 15 +PORTREVISION= 16 CATEGORIES= biology MASTER_SITES= SF/${PORTNAME}/ProtoMol/${PORTVERSION} DISTFILES= ${DISTNAME}-tar.gz diff --git a/biology/py-pyrodigal/Makefile b/biology/py-pyrodigal/Makefile index 29edb4cd9bf5..67eb9672b9b0 100644 --- a/biology/py-pyrodigal/Makefile +++ b/biology/py-pyrodigal/Makefile @@ -1,5 +1,5 @@ PORTNAME= pyrodigal -DISTVERSION= 3.3.0 +DISTVERSION= 3.4.0 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/py-pyrodigal/distinfo b/biology/py-pyrodigal/distinfo index a8d262237187..d3d07b0b3354 100644 --- a/biology/py-pyrodigal/distinfo +++ b/biology/py-pyrodigal/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1709932859 -SHA256 (pyrodigal-3.3.0.tar.gz) = 68f92cd83f9cd2883b99433847a827dd84ccb27edc51cb3f415664f0f08b0325 -SIZE (pyrodigal-3.3.0.tar.gz) = 2575105 +TIMESTAMP = 1716179060 +SHA256 (pyrodigal-3.4.0.tar.gz) = d4714e8f9208b7768f89bca9f47013e9f18f978e4baf43176a67af9cb26c7c79 +SIZE (pyrodigal-3.4.0.tar.gz) = 2577063 diff --git a/biology/py-pysam/Makefile b/biology/py-pysam/Makefile index 4435335a3a3b..745a4a165ed1 100644 --- a/biology/py-pysam/Makefile +++ b/biology/py-pysam/Makefile @@ -1,7 +1,8 @@ PORTNAME= pysam -DISTVERSION= 0.22.0 +DISTVERSIONPREFIX= v +DISTVERSION= 0.22.1 CATEGORIES= biology python -MASTER_SITES= PYPI +#MASTER_SITES= PYPI # no tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org @@ -12,14 +13,21 @@ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libhts.so:biology/htslib +RUN_DEPENDS= bcftools:biology/bcftools \ + samtools:biology/samtools USES= gmake python -USE_PYTHON= distutils autoplist cython cython_run +USE_PYTHON= distutils autoplist cython cython_run pytest # 2 failed, 155 errors, see https://github.com/pysam-developers/pysam/issues/1284 + +USE_GITHUB= yes +GH_ACCOUNT= pysam-developers BINARY_ALIAS= make=${GMAKE} MAKE_ENV= HTSLIB_MODE=external \ HTSLIB_LIBRARY_DIR=${LOCALBASE}/lib \ HTSLIB_INCLUDE_DIR=${LOCALBASE}/include +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 diff --git a/biology/py-pysam/distinfo b/biology/py-pysam/distinfo index 24a863205256..f5f1e4268139 100644 --- a/biology/py-pysam/distinfo +++ b/biology/py-pysam/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1696579895 -SHA256 (pysam-0.22.0.tar.gz) = ab7a46973cf0ab8c6ac327f4c3fb67698d7ccbeef8631a716898c6ba01ef3e45 -SIZE (pysam-0.22.0.tar.gz) = 4631254 +TIMESTAMP = 1714015094 +SHA256 (pysam-developers-pysam-v0.22.1_GH0.tar.gz) = e4981524d7627c53fa0d3f8cbec2bd65c2ea7520092f25e1029af12cb7b82ff6 +SIZE (pysam-developers-pysam-v0.22.1_GH0.tar.gz) = 3885851 diff --git a/biology/py-pysam/files/patch-setup.py b/biology/py-pysam/files/patch-setup.py deleted file mode 100644 index d82a8bbbefcf..000000000000 --- a/biology/py-pysam/files/patch-setup.py +++ /dev/null @@ -1,11 +0,0 @@ ---- setup.py.orig 2017-04-19 05:48:10 UTC -+++ setup.py -@@ -60,7 +60,7 @@ def run_configure(option): - - - def run_make_print_config(): -- stdout = subprocess.check_output(["make", "-s", "print-config"]) -+ stdout = subprocess.check_output(["gmake", "-s", "print-config"]) - if IS_PYTHON3: - stdout = stdout.decode("ascii") - diff --git a/biology/seqkit/Makefile b/biology/seqkit/Makefile index 09a2504dcd1e..e14200be2208 100644 --- a/biology/seqkit/Makefile +++ b/biology/seqkit/Makefile @@ -1,7 +1,6 @@ PORTNAME= seqkit DISTVERSIONPREFIX= v -DISTVERSION= 2.8.1 -PORTREVISION= 1 +DISTVERSION= 2.8.2 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/seqkit/distinfo b/biology/seqkit/distinfo index 03c82fc44ef4..050c34f956e4 100644 --- a/biology/seqkit/distinfo +++ b/biology/seqkit/distinfo @@ -1,7 +1,7 @@ -TIMESTAMP = 1712997584 -SHA256 (go/biology_seqkit/seqkit-v2.8.1/v2.8.1.mod) = 5a4eefdd7e32176c2f257c61a92713f1ed4198aa941ef7a9c2af5d3299b13832 -SIZE (go/biology_seqkit/seqkit-v2.8.1/v2.8.1.mod) = 2514 -SHA256 (go/biology_seqkit/seqkit-v2.8.1/v2.8.1.zip) = 9309215e79925c9c8348dbac4156f2bcf1e9cd933b1d1a9d8e0daa6c7a5b953a -SIZE (go/biology_seqkit/seqkit-v2.8.1/v2.8.1.zip) = 34091099 -SHA256 (go/biology_seqkit/seqkit-v2.8.1/golang-sys-v0.6.0_GH0.tar.gz) = b4f6d17c7a128f76169964b437cb66b3f2dbf9a33361928ec19dfecf7b03fc54 -SIZE (go/biology_seqkit/seqkit-v2.8.1/golang-sys-v0.6.0_GH0.tar.gz) = 1434234 +TIMESTAMP = 1716022666 +SHA256 (go/biology_seqkit/seqkit-v2.8.2/v2.8.2.mod) = 5a4eefdd7e32176c2f257c61a92713f1ed4198aa941ef7a9c2af5d3299b13832 +SIZE (go/biology_seqkit/seqkit-v2.8.2/v2.8.2.mod) = 2514 +SHA256 (go/biology_seqkit/seqkit-v2.8.2/v2.8.2.zip) = ab98d58be18e64aad44928254b939a09e92d7a21ca1d4a31a871ea4aac5e501b +SIZE (go/biology_seqkit/seqkit-v2.8.2/v2.8.2.zip) = 34091861 +SHA256 (go/biology_seqkit/seqkit-v2.8.2/golang-sys-v0.6.0_GH0.tar.gz) = b4f6d17c7a128f76169964b437cb66b3f2dbf9a33361928ec19dfecf7b03fc54 +SIZE (go/biology_seqkit/seqkit-v2.8.2/golang-sys-v0.6.0_GH0.tar.gz) = 1434234 diff --git a/biology/seqwish/Makefile b/biology/seqwish/Makefile index fe3f5e9f7965..1f3d5289ce30 100644 --- a/biology/seqwish/Makefile +++ b/biology/seqwish/Makefile @@ -1,6 +1,6 @@ PORTNAME= seqwish DISTVERSIONPREFIX= v -DISTVERSION= 0.7.9 +DISTVERSION= 0.7.10 CATEGORIES= biology MASTER_SITES= https://github.com/ekg/seqwish/releases/download/v${DISTVERSION}/ diff --git a/biology/seqwish/distinfo b/biology/seqwish/distinfo index 5753ca0fb6de..94a253bca889 100644 --- a/biology/seqwish/distinfo +++ b/biology/seqwish/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1689972439 -SHA256 (seqwish-v0.7.9.tar.gz) = 1ca7ebf02a35ad147c8a2b81f087aaba2deb878fec7acb4deb9f14e932e89d36 -SIZE (seqwish-v0.7.9.tar.gz) = 12116251 +TIMESTAMP = 1716052866 +SHA256 (seqwish-v0.7.10.tar.gz) = 133b32c9c99caf44eba955b74bae338681da78300e4b21269e07475f88c88b29 +SIZE (seqwish-v0.7.10.tar.gz) = 12125412 diff --git a/biology/star/Makefile b/biology/star/Makefile index 968caa762551..8e01f3198cd4 100644 --- a/biology/star/Makefile +++ b/biology/star/Makefile @@ -26,13 +26,14 @@ USE_GCC= yes USE_GITHUB= yes GH_ACCOUNT= alexdobin +EXTRACT_AFTER_ARGS= --exclude ${GH_PROJECT_DEFAULT}-${GH_TAGNAME_EXTRACT}/source/htslib --no-same-owner --no-same-permissions + WRKSRC_SUBDIR= source MAKE_FLAGS= HTSLIB='' CXXFLAGS_SIMD="" PLIST_FILES= bin/STAR post-patch: - ${RM} -rf ${WRKSRC}/htslib ${REINPLACE_CMD} \ -e 's|"htslib/htslib/sam.h"|<htslib/sam.h>|g' \ -e 's|"htslib/htslib/kstring.h"|<htslib/kstring.h>|g' \ diff --git a/biology/taxonkit/Makefile b/biology/taxonkit/Makefile index 4f09fafc7773..d76bd538eba1 100644 --- a/biology/taxonkit/Makefile +++ b/biology/taxonkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= taxonkit DISTVERSIONPREFIX= v DISTVERSION= 0.16.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/unikmer/Makefile b/biology/unikmer/Makefile index 5dd98ab42bb3..a032f583182a 100644 --- a/biology/unikmer/Makefile +++ b/biology/unikmer/Makefile @@ -1,7 +1,7 @@ PORTNAME= unikmer DISTVERSIONPREFIX= v DISTVERSION= 0.19.1 -PORTREVISION= 12 +PORTREVISION= 13 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile index 47503953ed1f..c4efb379e8f6 100644 --- a/biology/vcflib/Makefile +++ b/biology/vcflib/Makefile @@ -39,6 +39,7 @@ OPTIONS_SUB= yes ZIG_DESC= Include Zig language support +# FIXME: https://github.com/vcflib/vcflib/issues/399 ZIG_BUILD_DEPENDS= zig010>0:lang/zig010 CMAKE_ARGS+= -DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so diff --git a/biology/vsearch/Makefile b/biology/vsearch/Makefile index c42444db8a21..6d6ded03e517 100644 --- a/biology/vsearch/Makefile +++ b/biology/vsearch/Makefile @@ -1,6 +1,6 @@ PORTNAME= vsearch DISTVERSIONPREFIX= v -DISTVERSION= 2.27.1 +DISTVERSION= 2.28.1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/vsearch/distinfo b/biology/vsearch/distinfo index 7eea2ede671c..f746cec601da 100644 --- a/biology/vsearch/distinfo +++ b/biology/vsearch/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1712512768 -SHA256 (torognes-vsearch-v2.27.1_GH0.tar.gz) = 54666bcd9434fb7636c5b292a67e7c194e809e631bbe8f4f86b85fb47e863abc -SIZE (torognes-vsearch-v2.27.1_GH0.tar.gz) = 269179 +TIMESTAMP = 1714566699 +SHA256 (torognes-vsearch-v2.28.1_GH0.tar.gz) = 4f8bf0ad43fef77e573d152b59f55a1f81eb84c22d6545911757e6108f8de21c +SIZE (torognes-vsearch-v2.28.1_GH0.tar.gz) = 272918 |