diff --git a/biology/locarna/Makefile b/biology/locarna/Makefile index 53d51d26f8c8..a6c74fd931e6 100644 --- a/biology/locarna/Makefile +++ b/biology/locarna/Makefile @@ -1,37 +1,39 @@ PORTNAME= locarna DISTVERSION= 2.0.0 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= https://github.com/s-will/LocARNA/releases/download/v${DISTVERSION}/ MAINTAINER= yuri@FreeBSD.org COMMENT= LocARNA provides several tools for the structural analysis of RNA WWW= https://github.com/s-will/LocARNA LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= ${LOCALBASE}/lib/libRNA.a:biology/viennarna LIB_DEPENDS= libgmp.so:math/gmp \ libgsl.so:math/gsl \ libmpfr.so:math/mpfr TEST_DEPENDS= bash:shells/bash \ catch>0:devel/catch USES= autoreconf gmake libtool perl5 pkgconfig shebangfix USE_LDCONFIG= yes USE_CXXSTD= c++14 # workaround for https://github.com/s-will/LocARNA/issues/82 (LocARNA uses the removed STL method) CXXFLAGS+= -I${LOCALBASE}/include/catch2 # use external catch SHEBANG_FILES= src/Utils/locarna_mcc \ src/Tests/test_programs GNU_CONFIGURE= yes +GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share INSTALL_TARGET= install-strip TEST_TARGET= check # one test fails, see https://github.com/s-will/LocARNA/issues/81 post-extract: # unbundle catch, see https://github.com/s-will/LocARNA/issues/80 @${RM} ${WRKSRC}/src/Tests/catch.hpp .include diff --git a/biology/locarna/pkg-plist b/biology/locarna/pkg-plist index 0d6039099397..aaf183bf0bec 100644 --- a/biology/locarna/pkg-plist +++ b/biology/locarna/pkg-plist @@ -1,134 +1,134 @@ bin/LocARNA_RNAz.pm bin/RNAz.pm bin/aln-seqs.pl bin/aln2fa.pl bin/alnsel.pl bin/average-dot.pl bin/benchmark-plot.R bin/dot2pp bin/exparna_p bin/exploc_p bin/gen-reliab-dot.pl bin/locarna bin/locarna-mea.pl bin/locarna-motif-scan bin/locarna_deviation bin/locarna_mcc bin/locarna_p bin/locarna_rnafold_pp bin/locarnap-predict-and-plot.pl bin/locarnap-realign-all.pl bin/locarnap-revcomp.pl bin/locarnap-revisit-RNAz-hits.pl bin/locarnap_fit bin/locarnate bin/mlocarna bin/mlocarna_nnames bin/plot-bmprobs bin/pp2dot bin/reliability-profile.pl bin/ribosum2cc bin/sparse include/LocARNA-2.0/LocARNA/aligner.hh include/LocARNA-2.0/LocARNA/aligner_impl.hh include/LocARNA-2.0/LocARNA/aligner_n.hh include/LocARNA-2.0/LocARNA/aligner_p.hh include/LocARNA-2.0/LocARNA/aligner_p.icc include/LocARNA-2.0/LocARNA/aligner_params.hh include/LocARNA-2.0/LocARNA/aligner_restriction.hh include/LocARNA-2.0/LocARNA/alignment.hh include/LocARNA-2.0/LocARNA/alignment_impl.hh include/LocARNA-2.0/LocARNA/alphabet.hh include/LocARNA-2.0/LocARNA/alphabet.icc include/LocARNA-2.0/LocARNA/anchor_constraints.hh include/LocARNA-2.0/LocARNA/arc_matches.hh include/LocARNA-2.0/LocARNA/aux.hh include/LocARNA-2.0/LocARNA/base_pair_filter.hh include/LocARNA-2.0/LocARNA/basepairs.hh include/LocARNA-2.0/LocARNA/confusion_matrix.hh include/LocARNA-2.0/LocARNA/discrete_distribution.hh include/LocARNA-2.0/LocARNA/edge_probs.hh include/LocARNA-2.0/LocARNA/edge_probs.icc include/LocARNA-2.0/LocARNA/exact_matcher.hh include/LocARNA-2.0/LocARNA/ext_rna_data.hh include/LocARNA-2.0/LocARNA/ext_rna_data_impl.hh include/LocARNA-2.0/LocARNA/free_endgaps.hh include/LocARNA-2.0/LocARNA/global_stopwatch.hh include/LocARNA-2.0/LocARNA/infty_int.hh include/LocARNA-2.0/LocARNA/main_helper.icc include/LocARNA-2.0/LocARNA/matrices.hh include/LocARNA-2.0/LocARNA/matrix.hh include/LocARNA-2.0/LocARNA/mcc_matrices.hh include/LocARNA-2.0/LocARNA/multiple_alignment.hh include/LocARNA-2.0/LocARNA/named_arguments.hh include/LocARNA-2.0/LocARNA/options.hh include/LocARNA-2.0/LocARNA/pfold_params.hh include/LocARNA-2.0/LocARNA/quadmath.hh include/LocARNA-2.0/LocARNA/ribofit.hh include/LocARNA-2.0/LocARNA/ribofit_will2014.icc include/LocARNA-2.0/LocARNA/ribofit_will2014.ihh include/LocARNA-2.0/LocARNA/ribosum.hh include/LocARNA-2.0/LocARNA/ribosum85_60.icc include/LocARNA-2.0/LocARNA/rna_data.hh include/LocARNA-2.0/LocARNA/rna_data_impl.hh include/LocARNA-2.0/LocARNA/rna_ensemble.hh include/LocARNA-2.0/LocARNA/rna_ensemble_impl.hh include/LocARNA-2.0/LocARNA/rna_structure.hh include/LocARNA-2.0/LocARNA/scoring.hh include/LocARNA-2.0/LocARNA/scoring_fwd.hh include/LocARNA-2.0/LocARNA/sequence.hh include/LocARNA-2.0/LocARNA/sequence_annotation.hh include/LocARNA-2.0/LocARNA/sparse_matrix.hh include/LocARNA-2.0/LocARNA/sparse_vector.hh include/LocARNA-2.0/LocARNA/sparse_vector_base.hh include/LocARNA-2.0/LocARNA/sparsification_mapper.hh include/LocARNA-2.0/LocARNA/std_help_text.ihh include/LocARNA-2.0/LocARNA/stopwatch.hh include/LocARNA-2.0/LocARNA/stral_score.hh include/LocARNA-2.0/LocARNA/string1.hh include/LocARNA-2.0/LocARNA/trace_controller.hh include/LocARNA-2.0/LocARNA/tuples.hh include/LocARNA-2.0/LocARNA/zip.hh lib/libLocARNA-2.0.a lib/libLocARNA-2.0.so lib/libLocARNA-2.0.so.1 lib/libLocARNA-2.0.so.1.0.4 lib/perl/MLocarna.pm lib/perl/MLocarna/Aux.pm lib/perl/MLocarna/MatchProbs.pm lib/perl/MLocarna/NameNormalizer.pm lib/perl/MLocarna/PairwiseAligners.pm lib/perl/MLocarna/SparseMatrix.pm lib/perl/MLocarna/Tree.pm lib/perl/MLocarna/threaded.pm lib/perl/MLocarna/unthreaded.pm libdata/pkgconfig/LocARNA-2.0.pc -man/man1/aln-seqs.pl.1.gz -man/man1/aln2fa.pl.1.gz -man/man1/alnsel.pl.1.gz -man/man1/average-dot.pl.1.gz -man/man1/dot2pp.1.gz -man/man1/exparna_p.1.gz -man/man1/exploc_p.1.gz -man/man1/gen-reliab-dot.pl.1.gz -man/man1/locarna-mea.pl.1.gz -man/man1/locarna-motif-scan.1.gz -man/man1/locarna.1.gz -man/man1/locarna_deviation.1.gz -man/man1/locarna_mcc.1.gz -man/man1/locarna_p.1.gz -man/man1/locarna_rnafold_pp.1.gz -man/man1/locarnap-predict-and-plot.pl.1.gz -man/man1/locarnap-realign-all.pl.1.gz -man/man1/locarnap-revcomp.pl.1.gz -man/man1/locarnap-revisit-RNAz-hits.pl.1.gz -man/man1/locarnap_fit.1.gz -man/man1/locarnate.1.gz -man/man1/mlocarna.1.gz -man/man1/mlocarna_nnames.1.gz -man/man1/plot-bmprobs.1.gz -man/man1/pp2dot.1.gz -man/man1/reliability-profile.pl.1.gz -man/man1/ribosum2cc.1.gz -man/man1/sparse.1.gz +share/man/man1/aln-seqs.pl.1.gz +share/man/man1/aln2fa.pl.1.gz +share/man/man1/alnsel.pl.1.gz +share/man/man1/average-dot.pl.1.gz +share/man/man1/dot2pp.1.gz +share/man/man1/exparna_p.1.gz +share/man/man1/exploc_p.1.gz +share/man/man1/gen-reliab-dot.pl.1.gz +share/man/man1/locarna-mea.pl.1.gz +share/man/man1/locarna-motif-scan.1.gz +share/man/man1/locarna.1.gz +share/man/man1/locarna_deviation.1.gz +share/man/man1/locarna_mcc.1.gz +share/man/man1/locarna_p.1.gz +share/man/man1/locarna_rnafold_pp.1.gz +share/man/man1/locarnap-predict-and-plot.pl.1.gz +share/man/man1/locarnap-realign-all.pl.1.gz +share/man/man1/locarnap-revcomp.pl.1.gz +share/man/man1/locarnap-revisit-RNAz-hits.pl.1.gz +share/man/man1/locarnap_fit.1.gz +share/man/man1/locarnate.1.gz +share/man/man1/mlocarna.1.gz +share/man/man1/mlocarna_nnames.1.gz +share/man/man1/plot-bmprobs.1.gz +share/man/man1/pp2dot.1.gz +share/man/man1/reliability-profile.pl.1.gz +share/man/man1/ribosum2cc.1.gz +share/man/man1/sparse.1.gz %%DATADIR%%/Matrices/RIBOSUM85_60