diff --git a/biology/viennarna/Makefile b/biology/viennarna/Makefile index d24e3125f5f2..fbf0bae747ed 100644 --- a/biology/viennarna/Makefile +++ b/biology/viennarna/Makefile @@ -1,46 +1,50 @@ PORTNAME= viennarna DISTVERSION= 2.6.2 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_6_x/ DISTNAME= ViennaRNA-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Alignment tools for the structural analysis of RNA WWW= https://www.tbi.univie.ac.at/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 \ liblapack.so:math/lapack \ libmpfr.so:math/mpfr \ libopenblas.so:math/openblas USES= autoreconf compiler:c++11-lang fortran gmake libtool localbase perl5 pkgconfig xorg # w/out autoreconf -lstdc++ is present in configure and Makefiles and this causes link failure 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 TEST_TARGET= check CONFLICTS_INSTALL= g2 # include/g2.h INFO= RNAlib DATASDIR= ${PREFIX}/share/ViennaRNA DOCSDIR= ${PREFIX}/share/doc/ViennaRNA EXAMPLESDIR= ${PREFIX}/share/examples/ViennaRNA OPTIONS_DEFINE= DOCS EXAMPLES PORTDOCS= * PORTEXAMPLES= * +post-configure: # remove -lstdc++ from .pc file + @${REINPLACE_CMD} -e 's| -lstdc++||' ${WRKSRC}/RNAlib2.pc + .include diff --git a/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am b/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am index 170cccfc6eb7..8857bf17c682 100644 --- a/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am +++ b/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am @@ -1,11 +1,11 @@ ---- RNA-Tutorial/Makefile.am.orig 2019-06-24 18:48:09 UTC +--- RNA-Tutorial/Makefile.am.orig 2020-11-23 22:41:05 UTC +++ RNA-Tutorial/Makefile.am -@@ -95,7 +95,7 @@ vrna_htmltutorial_uninst: +@@ -90,7 +90,7 @@ vrna_htmltutorial_uninst: if WITH_TUTORIAL_PDF -tut_datadir = $(pkgdatadir)/tutorial +tut_datadir = $(prefix)/share/doc/ViennaRNA/tutorial tut_programsdir = $(tut_datadir)/programs tut_alifoldzdir = $(tut_datadir)/alifoldz tut_qrnadir = $(tut_datadir)/qrna diff --git a/biology/viennarna/pkg-descr b/biology/viennarna/pkg-descr index dd5376f2a390..acceb30f5685 100644 --- a/biology/viennarna/pkg-descr +++ b/biology/viennarna/pkg-descr @@ -1,13 +1,14 @@ -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. +The ViennaRNA Package consists of a C code library and several stand-alone +programs for the prediction and comparison of RNA secondary structures. -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. +RNA secondary structure prediction through energy minimization is the most used +function in the package. We provide three kinds of dynamic programming +algorithms for structure prediction: the minimum free energy algorithm of +(Zuker & Stiegler 1981) which yields a single optimal structure, the partition +function algorithm of (McCaskill 1990) which calculates base pair probabilities +in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty +et.al 1999) which generates all suboptimal structures within a given energy +range of the optimal energy. For secondary structure comparison, the package +contains several measures of distance (dissimilarities) using either string +alignment or tree-editing (Shapiro & Zhang 1990). Finally, we provide an +algorithm to design sequences with a predefined structure (inverse folding).