git: 5560f5f4c85f - main - biology/locarna: New port: LocARNA provides several tools for the structural analysis of RNA

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sun, 16 Jul 2023 21:55:25 UTC
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