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New port: biology/viennarna: Alignment tools for the structural analysis of RNA

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This commit is contained in:
Yuri Victorovich 2019-06-24 09:29:05 +00:00
parent e1a267fb0d
commit f848ca2897
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=505017
9 changed files with 331 additions and 0 deletions
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1
biology/Makefile
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@ -164,6 +164,7 @@
SUBDIR += vcflib
SUBDIR += vcftools
SUBDIR += velvet
SUBDIR += viennarna
SUBDIR += vsearch
SUBDIR += wise

41
biology/viennarna/Makefile Normal file
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@ -0,0 +1,41 @@
# $FreeBSD$
PORTNAME= viennarna
DISTVERSION= 2.4.13
CATEGORIES= biology
MASTER_SITES= https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/
DISTNAME= ViennaRNA-${DISTVERSION}
MAINTAINER= yuri@FreeBSD.org
COMMENT= Alignment tools for the structural analysis of RNA
LICENSE= ViennaRNALicense
LICENSE_NAME= Vienna RNA License
LICENSE_FILE= ${WRKSRC}/COPYING
LICENSE_PERMS= auto-accept dist-mirror pkg-mirror
BUILD_DEPENDS= bash:shells/bash \
libgd>0:graphics/gd # for the static lib
LIB_DEPENDS= libgmp.so:math/gmp \
libgsl.so:math/gsl \
libmpfr.so:math/mpfr
USES= compiler:c++11-lang gmake libtool localbase perl5
USE_XORG= x11 xext # only for build
GNU_CONFIGURE= yes
CONFIGURE_SHELL= ${PREFIX}/bin/bash
CONFIGURE_ARGS= --enable-shared --disable-static --with-gsl --with-cluster --with-kinwalker --enable-mpfr --without-python --without-python3 --without-perl
INFO= RNAlib
DATASDIR= ${PREFIX}/share/ViennaRNA
DOCSDIR= ${PREFIX}/share/doc/ViennaRNA
EXAMPLESDIR= ${PREFIX}/share/examples/ViennaRNA
OPTIONS_DEFINE= DOCS EXAMPLES
PORTDOCS= *
PORTEXAMPLES= *
.include <bsd.port.mk>

3
biology/viennarna/distinfo Normal file
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@ -0,0 +1,3 @@
TIMESTAMP = 1561312270
SHA256 (ViennaRNA-2.4.13.tar.gz) = 915c271b48536a3cc60b3109f11f7fd99dcd26d22621ee50f05e7f1c2f90cabe
SIZE (ViennaRNA-2.4.13.tar.gz) = 34094932

11
biology/viennarna/files/patch-RNA-Tutorial_Makefile.in Normal file
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@ -0,0 +1,11 @@
--- RNA-Tutorial/Makefile.in.orig 2019-06-24 07:18:45 UTC
+++ RNA-Tutorial/Makefile.in
@@ -459,7 +459,7 @@ clean_tutorial_html = rm -f *.html *.css *.4ct *.4tc *
@WITH_TUTORIAL_BUILD_TRUE@@WITH_TUTORIAL_PDFLATEX_FALSE@@WITH_TUTORIAL_PDF_TRUE@@WITH_TUTORIAL_TRUE@CONVERT_TUT_TO_PDF = $(TUTORIAL_CMD_DVIPDF) tutorial.dvi;
html_DATA = $(TUTORIAL_FILES_HTML)
pdf_DATA = $(TUTORIAL_FILES_PDF)
-@WITH_TUTORIAL_PDF_TRUE@tut_datadir = $(pkgdatadir)/tutorial
+@WITH_TUTORIAL_PDF_TRUE@tut_datadir = $(prefix)/share/doc/ViennaRNA/tutorial
@WITH_TUTORIAL_PDF_TRUE@tut_programsdir = $(tut_datadir)/programs
@WITH_TUTORIAL_PDF_TRUE@tut_alifoldzdir = $(tut_datadir)/alifoldz
@WITH_TUTORIAL_PDF_TRUE@tut_qrnadir = $(tut_datadir)/qrna

11
biology/viennarna/files/patch-configure Normal file
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@ -0,0 +1,11 @@
--- configure.orig 2019-05-31 13:31:21 UTC
+++ configure
@@ -22325,7 +22325,7 @@ fi
if test "x$enable_static_executables" = "xyes"; then
SAVED_LDFLAGS=$LDFLAGS
- LDFLAGS="$LDFLAGS -static -lstdc++"
+ LDFLAGS="$LDFLAGS -static -lc++"
{ $as_echo "$as_me:${as_lineno-$LINENO}: Checking possiblity to build statically linked executables using C++ compiler" >&5
$as_echo "$as_me: Checking possiblity to build statically linked executables using C++ compiler" >&6;}

11
biology/viennarna/files/patch-examples_Makefile.in Normal file
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@ -0,0 +1,11 @@
--- examples/Makefile.in.orig 2019-06-24 07:09:07 UTC
+++ examples/Makefile.in
@@ -441,7 +441,7 @@ target_alias = @target_alias@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
-pkgexampledir = $(pkgdatadir)/examples
+pkgexampledir = $(prefix)/share/examples/ViennaRNA
pkgexampledatadir = $(pkgexampledir)/data
pkgperlexampledir = $(pkgexampledir)/perl5
pkgpythonexampledir = $(pkgexampledir)/python

13
biology/viennarna/files/patch-src_bin_Makefile.in Normal file
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@ -0,0 +1,13 @@
--- src/bin/Makefile.in.orig 2019-06-24 04:33:32 UTC
+++ src/bin/Makefile.in
@@ -104,8 +104,8 @@ bin_PROGRAMS = RNAfold$(EXEEXT) RNAeval$(EXEEXT) RNAhe
RNAparconv$(EXEEXT) RNAPKplex$(EXEEXT) RNAplex$(EXEEXT) \
RNAsnoop$(EXEEXT) RNApvmin$(EXEEXT)
@VRNA_AM_SWITCH_MPFR_TRUE@am__append_4 = $(MPFR_LIBS)
-@VRNA_AM_SWITCH_SVM_TRUE@am__append_5 = -lstdc++
-@VRNA_AM_SWITCH_SVM_TRUE@am__append_6 = -lstdc++
+@VRNA_AM_SWITCH_SVM_TRUE@am__append_5 = -lc++
+@VRNA_AM_SWITCH_SVM_TRUE@am__append_6 = -lc++
subdir = src/bin
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/m4/ac_rna.m4 \

15
biology/viennarna/pkg-descr Normal file
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@ -0,0 +1,15 @@
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.
WWW: https://github.com/s-will/LocARNA

225
biology/viennarna/pkg-plist Normal file
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@ -0,0 +1,225 @@
bin/AnalyseDists
bin/AnalyseSeqs
bin/Kinfold
bin/RNA2Dfold
bin/RNALalifold
bin/RNALfold
bin/RNAPKplex
bin/RNAaliduplex
bin/RNAalifold
bin/RNAcofold
bin/RNAdistance
bin/RNAduplex
bin/RNAeval
bin/RNAfold
bin/RNAforester
bin/RNAheat
bin/RNAinverse
bin/RNAlocmin
bin/RNApaln
bin/RNAparconv
bin/RNApdist
bin/RNAplex
bin/RNAplfold
bin/RNAplot
bin/RNApvmin
bin/RNAsnoop
bin/RNAsubopt
bin/RNAup
bin/b2ct
bin/ct2db
bin/kinwalker
bin/popt
include/ViennaRNA/2Dfold.h
include/ViennaRNA/2Dpfold.h
include/ViennaRNA/LPfold.h
include/ViennaRNA/Lfold.h
include/ViennaRNA/MEA.h
include/ViennaRNA/PKplex.h
include/ViennaRNA/PS_dot.h
include/ViennaRNA/ProfileAln.h
include/ViennaRNA/RNAstruct.h
include/ViennaRNA/ali_plex.h
include/ViennaRNA/alifold.h
include/ViennaRNA/aln_util.h
include/ViennaRNA/alphabet.h
include/ViennaRNA/boltzmann_sampling.h
include/ViennaRNA/centroid.h
include/ViennaRNA/char_stream.h
include/ViennaRNA/cofold.h
include/ViennaRNA/combinatorics.h
include/ViennaRNA/commands.h
include/ViennaRNA/concentrations.h
include/ViennaRNA/constraints.h
include/ViennaRNA/constraints/SHAPE.h
include/ViennaRNA/constraints/basic.h
include/ViennaRNA/constraints/hard.h
include/ViennaRNA/constraints/ligand.h
include/ViennaRNA/constraints/soft.h
include/ViennaRNA/constraints_SHAPE.h
include/ViennaRNA/constraints_hard.h
include/ViennaRNA/constraints_ligand.h
include/ViennaRNA/constraints_soft.h
include/ViennaRNA/convert_epars.h
include/ViennaRNA/data_structures.h
include/ViennaRNA/datastructures/basic.h
include/ViennaRNA/datastructures/char_stream.h
include/ViennaRNA/datastructures/hash_tables.h
include/ViennaRNA/datastructures/heap.h
include/ViennaRNA/datastructures/lists.h
include/ViennaRNA/datastructures/stream_output.h
include/ViennaRNA/dist_vars.h
include/ViennaRNA/dp_matrices.h
include/ViennaRNA/duplex.h
include/ViennaRNA/edit_cost.h
include/ViennaRNA/energy_const.h
include/ViennaRNA/energy_par.h
include/ViennaRNA/equilibrium_probs.h
include/ViennaRNA/eval.h
include/ViennaRNA/exterior_loops.h
include/ViennaRNA/file_formats.h
include/ViennaRNA/file_formats_msa.h
include/ViennaRNA/file_utils.h
include/ViennaRNA/findpath.h
include/ViennaRNA/fold.h
include/ViennaRNA/fold_compound.h
include/ViennaRNA/fold_vars.h
include/ViennaRNA/gquad.h
include/ViennaRNA/grammar.h
include/ViennaRNA/hairpin_loops.h
include/ViennaRNA/interior_loops.h
include/ViennaRNA/inverse.h
include/ViennaRNA/io/file_formats.h
include/ViennaRNA/io/file_formats_msa.h
include/ViennaRNA/io/utils.h
include/ViennaRNA/json.h
include/ViennaRNA/landscape/findpath.h
include/ViennaRNA/landscape/move.h
include/ViennaRNA/landscape/neighbor.h
include/ViennaRNA/landscape/paths.h
include/ViennaRNA/landscape/walk.h
include/ViennaRNA/loop_energies.h
include/ViennaRNA/loops/all.h
include/ViennaRNA/loops/external.h
include/ViennaRNA/loops/hairpin.h
include/ViennaRNA/loops/internal.h
include/ViennaRNA/loops/multibranch.h
include/ViennaRNA/mfe.h
include/ViennaRNA/mfe_window.h
include/ViennaRNA/mm.h
include/ViennaRNA/model.h
include/ViennaRNA/move_set.h
include/ViennaRNA/multibranch_loops.h
include/ViennaRNA/naview.h
include/ViennaRNA/neighbor.h
include/ViennaRNA/pair_mat.h
include/ViennaRNA/params.h
include/ViennaRNA/params/basic.h
include/ViennaRNA/params/constants.h
include/ViennaRNA/params/convert.h
include/ViennaRNA/params/default.h
include/ViennaRNA/params/io.h
include/ViennaRNA/part_func.h
include/ViennaRNA/part_func_co.h
include/ViennaRNA/part_func_up.h
include/ViennaRNA/part_func_window.h
include/ViennaRNA/perturbation_fold.h
include/ViennaRNA/plex.h
include/ViennaRNA/plot_aln.h
include/ViennaRNA/plot_layouts.h
include/ViennaRNA/plot_structure.h
include/ViennaRNA/plot_utils.h
include/ViennaRNA/plotting/RNApuzzler/RNApuzzler.h
include/ViennaRNA/plotting/RNApuzzler/RNAturtle.h
include/ViennaRNA/plotting/alignments.h
include/ViennaRNA/plotting/layouts.h
include/ViennaRNA/plotting/naview.h
include/ViennaRNA/plotting/probabilities.h
include/ViennaRNA/plotting/structures.h
include/ViennaRNA/plotting/utils.h
include/ViennaRNA/profiledist.h
include/ViennaRNA/read_epars.h
include/ViennaRNA/ribo.h
include/ViennaRNA/search/BoyerMoore.h
include/ViennaRNA/sequence.h
include/ViennaRNA/snofold.h
include/ViennaRNA/snoop.h
include/ViennaRNA/stream_output.h
include/ViennaRNA/string_utils.h
include/ViennaRNA/stringdist.h
include/ViennaRNA/structure_utils.h
include/ViennaRNA/structured_domains.h
include/ViennaRNA/subopt.h
include/ViennaRNA/svm.h
include/ViennaRNA/svm_utils.h
include/ViennaRNA/treedist.h
include/ViennaRNA/units.h
include/ViennaRNA/unstructured_domains.h
include/ViennaRNA/utils.h
include/ViennaRNA/utils/alignments.h
include/ViennaRNA/utils/basic.h
include/ViennaRNA/utils/cpu.h
include/ViennaRNA/utils/higher_order_functions.h
include/ViennaRNA/utils/strings.h
include/ViennaRNA/utils/structures.h
include/ViennaRNA/utils/svm.h
include/ViennaRNA/vrna_config.h
include/ViennaRNA/walk.h
include/g2.h
include/g2_FIG.h
include/g2_PS.h
include/g2_X11.h
include/g2_gd.h
lib/libRNA.a
lib/libg2.a
libdata/pkgconfig/RNAlib2.pc
man/man1/AnalyseDists.1.gz
man/man1/AnalyseSeqs.1.gz
man/man1/Kinfold.1.gz
man/man1/RNA2Dfold.1.gz
man/man1/RNALalifold.1.gz
man/man1/RNALfold.1.gz
man/man1/RNAPKplex.1.gz
man/man1/RNAaliduplex.1.gz
man/man1/RNAalifold.1.gz
man/man1/RNAcofold.1.gz
man/man1/RNAdistance.1.gz
man/man1/RNAduplex.1.gz
man/man1/RNAeval.1.gz
man/man1/RNAfold.1.gz
man/man1/RNAforester.1.gz
man/man1/RNAheat.1.gz
man/man1/RNAinverse.1.gz
man/man1/RNAlocmin.1.gz
man/man1/RNApaln.1.gz
man/man1/RNAparconv.1.gz
man/man1/RNApdist.1.gz
man/man1/RNAplex.1.gz
man/man1/RNAplfold.1.gz
man/man1/RNAplot.1.gz
man/man1/RNApvmin.1.gz
man/man1/RNAsnoop.1.gz
man/man1/RNAsubopt.1.gz
man/man1/RNAup.1.gz
man/man1/ct2db.1.gz
man/man1/kinwalker.1.gz
share/ViennaRNA/2Dlandscape_mfe.gri
share/ViennaRNA/2Dlandscape_pf.gri
share/ViennaRNA/DoxygenLayout.xml
share/ViennaRNA/bin/RNAdesign.pl
share/ViennaRNA/bin/b2mt.pl
share/ViennaRNA/bin/cmount.pl
share/ViennaRNA/bin/coloraln.pl
share/ViennaRNA/bin/dpzoom.pl
share/ViennaRNA/bin/mountain.pl
share/ViennaRNA/bin/refold.pl
share/ViennaRNA/bin/relplot.pl
share/ViennaRNA/bin/rotate_ss.pl
share/ViennaRNA/bin/switch.pl
share/ViennaRNA/dna_mathews1999.par
share/ViennaRNA/dna_mathews2004.par
share/ViennaRNA/rna_andronescu2007.par
share/ViennaRNA/rna_langdon2018.par
share/ViennaRNA/rna_turner1999.par
share/ViennaRNA/rna_turner2004.par
share/ViennaRNA/viennarna.bib