Date: Sun, 16 Jul 2023 21:55:25 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 5560f5f4c85f - main - biology/locarna: New port: LocARNA provides several tools for the structural analysis of RNA Message-ID: <202307162155.36GLtPkC009607@gitrepo.freebsd.org>
next in thread | raw e-mail | index | archive | help
The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=5560f5f4c85f3231d66a7109ff611ab6870292e8 commit 5560f5f4c85f3231d66a7109ff611ab6870292e8 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2023-07-16 21:54:52 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2023-07-16 21:54:52 +0000 biology/locarna: New port: LocARNA provides several tools for the structural analysis of RNA --- biology/Makefile | 1 + biology/locarna/Makefile | 28 ++++++++++ biology/locarna/distinfo | 3 ++ biology/locarna/pkg-descr | 13 +++++ biology/locarna/pkg-plist | 134 ++++++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 179 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 71d625b98e9f..e41e9edcb828 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -95,6 +95,7 @@ SUBDIR += libsbml SUBDIR += libsedml SUBDIR += linux-foldingathome + SUBDIR += locarna SUBDIR += mafft SUBDIR += mapm3 SUBDIR += mashmap diff --git a/biology/locarna/Makefile b/biology/locarna/Makefile new file mode 100644 index 000000000000..6c6c008b2384 --- /dev/null +++ b/biology/locarna/Makefile @@ -0,0 +1,28 @@ +PORTNAME= locarna +DISTVERSION= 2.0.0 +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 + +USES= autoreconf gmake libtool perl5 pkgconfig shebangfix +USE_LDCONFIG= yes + +SHEBANG_FILES= src/Utils/locarna_mcc + +GNU_CONFIGURE= yes + +INSTALL_TARGET= install-strip +TEST_TARGET= check # tests fail to compile, see https://github.com/s-will/LocARNA/issues/80 + +.include <bsd.port.mk> diff --git a/biology/locarna/distinfo b/biology/locarna/distinfo new file mode 100644 index 000000000000..1b872dee9ea6 --- /dev/null +++ b/biology/locarna/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1689540878 +SHA256 (locarna-2.0.0.tar.gz) = 3be0d2cac7f7451f8b741983e22803b546de2074d837b425fb1b69ccc718ebbc +SIZE (locarna-2.0.0.tar.gz) = 3049455 diff --git a/biology/locarna/pkg-descr b/biology/locarna/pkg-descr new file mode 100644 index 000000000000..dd5376f2a390 --- /dev/null +++ b/biology/locarna/pkg-descr @@ -0,0 +1,13 @@ +LocARNA is a collection of alignment tools for the structural analysis of RNA. +Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common +structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment +and is in particular suited for analyzing sets of related RNAs without known +common structure. + +LocARNA distinguishes itself from many other Sankoff-style multiple alignment +programs by its performance and low memory complexity, high accuracy, and +richness of features. As unique features, it offers structure-local alignment, +flexible structure and anchor constraints, and provides efficient computation of +reliabilities in sequence-structure alignment. The package offers a robust core +of features and is used as experimental platform for the incorporation of new +features in RNA sequence-structure alignment. diff --git a/biology/locarna/pkg-plist b/biology/locarna/pkg-plist new file mode 100644 index 000000000000..0d6039099397 --- /dev/null +++ b/biology/locarna/pkg-plist @@ -0,0 +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 +%%DATADIR%%/Matrices/RIBOSUM85_60
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202307162155.36GLtPkC009607>