BSD Portsbiology/locarna 2.0.1 FreeBSD
LocARNA provides several tools for the structural analysis of RNA
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- GPLv3
- Categories
- biology
- Package size
- 1902.7 KiB, 25245.1 KiB installed
Description
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.
In the other systems
The newest version among them is 2.0.1, as upstream numbers it.
| System | Port | Version | Vulnerabilities | Status | Maintainer | Last update |
|---|---|---|---|---|---|---|
| FreeBSD | biology/locarna | 2.0.1 newest | none known | - | [email protected] | - |
| HardenedBSD | biology/locarna | 2.0.1 newest | no data | - | [email protected] | - |
| GhostBSD | biology/locarna | 2.0.1 newest | no data | - | [email protected] | - |
Install
Binary package:
pkg install locarnaFrom the ports tree:
cd /usr/ports/biology/locarna/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= locarna>0:biology/locarna
LIB_DEPENDS= libLocARNA-2.0.so:biology/locarnaPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 2.0.1 | 2.0.1 | - | 2.0.0_1 | 2.0.1 |
| FreeBSD:14:quarterly | 2.0.1 | 2.0.1 | n/a | 2.0.0_1 | 2.0.1 |
| FreeBSD:15:latest | 2.0.1 | 2.0.1 | n/a | - | - |
| FreeBSD:15:quarterly | 2.0.1 | 2.0.1 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.0.1 | 2.0.1 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependency graph
Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.
Dependencies
As this port's Makefile names them.
Build 1
${LOCALBASE}/lib/libRNA.a: biology/viennarna
Library 3
Test 2
bash: shells/bashcatch>0: devel/catch
The full lists below include those, and their dependencies in turn.
Build dependencies 37
- archivers/liblz4
- archivers/zstd
- biology/viennarna
- databases/sqlite3
- devel/autoconf
- devel/autoconf-switch
- devel/automake
- devel/binutils
- devel/gettext-runtime
- devel/gmake
- devel/libedit
- devel/libtool
- devel/m4
- devel/pkgconf
- graphics/giflib
- graphics/jpeg-turbo
- graphics/png
- lang/gcc14
- lang/perl5.42
- lang/tcl86
- math/blas
- math/gmp
- math/gsl
- math/lapack
- math/libtommath
- math/mpc
- math/mpfr
- print/indexinfo
- science/dlib-cpp
- x11/libICE
- x11/libSM
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libxcb
- x11/xorgproto
Run dependencies 5
No port depends on this one.
Configuration
No options to configure.
- USES
- autoreconf gmake libtool perl5 pkgconfig shebangfix
- Service scripts
- none
Files
Manual pages 28
- aln-seqs.pl(1)
- aln2fa.pl(1)
- alnsel.pl(1)
- average-dot.pl(1)
- dot2pp(1)
- exparna_p(1)
- exploc_p(1)
- gen-reliab-dot.pl(1)
- locarna(1)
- locarna-mea.pl(1)
- locarna-motif-scan(1)
- locarna_deviation(1)
- locarna_mcc(1)
- locarna_p(1)
- locarna_rnafold_pp(1)
- locarnap-predict-and-plot.pl(1)
- locarnap-realign-all.pl(1)
- locarnap-revcomp.pl(1)
- locarnap-revisit-RNAz-hits.pl(1)
- locarnap_fit(1)
- locarnate(1)
- mlocarna(1)
- mlocarna_nnames(1)
- plot-bmprobs(1)
- pp2dot(1)
- reliability-profile.pl(1)
- ribosum2cc(1)
- sparse(1)
pkg-plist 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
The first 100 are listed.
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| locarna-2.0.1.tar.gz | 3.135134e+06 | 1f50748d2f8f4bf5888394154d366e0eed8d4e20a3cd0da8b33e200aa1d9edf7 |
Master sites 1
- https://github.com/s-will/LocARNA/releases/download/v2.0.1/
Commit history 0
No commits in the history this site was built from.