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biology/locarna: New port: LocARNA provides several tools for the structural analysis of RNA

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This commit is contained in:
Yuri Victorovich 2023-07-16 14:54:52 -07:00
parent 3e4f91e805
commit 5560f5f4c8
5 changed files with 179 additions and 0 deletions
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1
biology/Makefile
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@ -95,6 +95,7 @@
SUBDIR += libsbml
SUBDIR += libsedml
SUBDIR += linux-foldingathome
SUBDIR += locarna
SUBDIR += mafft
SUBDIR += mapm3
SUBDIR += mashmap

28
biology/locarna/Makefile Normal file
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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>

3
biology/locarna/distinfo Normal file
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@ -0,0 +1,3 @@
TIMESTAMP = 1689540878
SHA256 (locarna-2.0.0.tar.gz) = 3be0d2cac7f7451f8b741983e22803b546de2074d837b425fb1b69ccc718ebbc
SIZE (locarna-2.0.0.tar.gz) = 3049455

13
biology/locarna/pkg-descr Normal file
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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.

134
biology/locarna/pkg-plist Normal file
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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