Date: Sun, 16 Jul 2023 21:55:24 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 3e4f91e805a3 - main - biology/viennarna: Remove unnecessary library from .pc file; Correct pkg-descr Message-ID: <202307162155.36GLtOni009582@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=3e4f91e805a3663672f9efdae1d4bb5b44d0c81a commit 3e4f91e805a3663672f9efdae1d4bb5b44d0c81a Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2023-07-16 21:38:39 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2023-07-16 21:38:39 +0000 biology/viennarna: Remove unnecessary library from .pc file; Correct pkg-descr --- biology/viennarna/Makefile | 4 ++++ .../viennarna/files/patch-RNA-Tutorial_Makefile.am | 4 ++-- biology/viennarna/pkg-descr | 25 +++++++++++----------- 3 files changed, 19 insertions(+), 14 deletions(-) diff --git a/biology/viennarna/Makefile b/biology/viennarna/Makefile index d24e3125f5f2..fbf0bae747ed 100644 --- a/biology/viennarna/Makefile +++ b/biology/viennarna/Makefile @@ -1,5 +1,6 @@ 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-${DISTVERSION} @@ -43,4 +44,7 @@ OPTIONS_DEFINE= DOCS EXAMPLES PORTDOCS= * PORTEXAMPLES= * +post-configure: # remove -lstdc++ from .pc file + @${REINPLACE_CMD} -e 's| -lstdc++||' ${WRKSRC}/RNAlib2.pc + .include <bsd.port.mk> 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 @@ -1,6 +1,6 @@ ---- 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 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).
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