diff options
Diffstat (limited to 'academic/ViennaRNA')
| -rw-r--r-- | academic/ViennaRNA/README | 33 | ||||
| -rw-r--r-- | academic/ViennaRNA/ViennaRNA.SlackBuild | 2 | ||||
| -rw-r--r-- | academic/ViennaRNA/ViennaRNA.info | 8 | ||||
| -rw-r--r-- | academic/ViennaRNA/slack-desc | 4 |
4 files changed, 25 insertions, 22 deletions
diff --git a/academic/ViennaRNA/README b/academic/ViennaRNA/README index 6ad531d628..a82c7160b2 100644 --- a/academic/ViennaRNA/README +++ b/academic/ViennaRNA/README @@ -7,8 +7,9 @@ A tutorial (see /usr/doc/$PRGNAM-$VERSION/RNA-tutorial-$VERSION.pdf) and examples can be found in /usr/share/$PRGNAM/tutorial and /usr/share/$PRGNAM/examples -For those who wish to link the Vienna package to their own C, perl or python programs (see below), -the RNAlib Reference Manual can be assessed at: +For those who wish to link the Vienna package to their own C, perl +or python programs (see below), the RNAlib Reference Manual can be +assessed at: https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/index.html (or unpacked from the src: $PRGNAM-$VERSION/doc/html/) @@ -22,29 +23,31 @@ Amongst other things, the ViennRNA implementations allow you to: - compute various equilibrium probabilities - calculate suboptimal structures in a given energy range - compute local structures in long sequences -- predict consensus secondary structures from a multiple sequence alignment +- predict consensus secondary structures from a multiple sequence + alignment - predict melting curves - search for sequences folding into a given structure - compare two secondary structures - predict hybridization structures of two RNA molecules -The package includes `Perl 5` and `Python 3` modules that give -access to almost all functions of the C library from within the respective +The package includes `Perl 5` and `Python 3` modules that give access +to almost all functions of the C library from within the respective scripting languages. For this reason, python3 is a dependency -The `Python 2` module can be built as well, or instead of the one for `Python 3`; -just edit the SlackBuild or run it by setting build options PYTHON=yes PYTHON3=no. -(e.g. in sbopkg or run it from the commandline -within the directory containing -the SlackBuild script and downloaded source archive- as: -`PYTHON=yes PYTHON3=no ./ViennaRNA.SlackBuild`) +The `Python 2` module can be built as well, or instead of the one +for `Python 3`; just edit the SlackBuild or run it by setting build +options PYTHON=yes PYTHON3=no. (e.g. in sbopkg or run it from +the commandline -within the directory containing the SlackBuild +script and downloaded source archive- as: `PYTHON=yes PYTHON3=no +./ViennaRNA.SlackBuild`) There is also a set of programs for analyzing sequence and distance -data using split decomposition, statistical geometry, and cluster methods. -They are not maintained any more and not built by default. +data using split decomposition, statistical geometry, and cluster +methods. They are not maintained any more and not built by default. -The code very rarely uses static arrays, and all programs should work for -sequences up to a length of 32,700 (if you have huge amounts of memory that -is). +The code very rarely uses static arrays, and all programs should work +for sequences up to a length of 32,700 (if you have huge amounts of +memory that is). For further info see: diff --git a/academic/ViennaRNA/ViennaRNA.SlackBuild b/academic/ViennaRNA/ViennaRNA.SlackBuild index ff63062efc..8bc20e2a45 100644 --- a/academic/ViennaRNA/ViennaRNA.SlackBuild +++ b/academic/ViennaRNA/ViennaRNA.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=ViennaRNA -VERSION=${VERSION:-2.4.14} +VERSION=${VERSION:-2.4.17} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/ViennaRNA/ViennaRNA.info b/academic/ViennaRNA/ViennaRNA.info index 06e2675530..162b17f93a 100644 --- a/academic/ViennaRNA/ViennaRNA.info +++ b/academic/ViennaRNA/ViennaRNA.info @@ -1,10 +1,10 @@ PRGNAM="ViennaRNA" -VERSION="2.4.14" +VERSION="2.4.17" HOMEPAGE="https://www.tbi.univie.ac.at/RNA" -DOWNLOAD="https://github.com/ViennaRNA/ViennaRNA/releases/download/v2.4.14/ViennaRNA-2.4.14.tar.gz" -MD5SUM="b9c64be709d3dfef72cc27e615845a04" +DOWNLOAD="https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.17.tar.gz" +MD5SUM="16bc4e1889c301b91985a3bac1f21e30" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="python3 gri" +REQUIRES="python3" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/ViennaRNA/slack-desc b/academic/ViennaRNA/slack-desc index e5d1921f61..5e5f6be6ea 100644 --- a/academic/ViennaRNA/slack-desc +++ b/academic/ViennaRNA/slack-desc @@ -6,13 +6,13 @@ # customary to leave one space after the ':' except on otherwise blank lines. |-----handy-ruler------------------------------------------------------| -ViennaRNA: VienaRNA (C Library) +ViennaRNA: ViennaRNA (C Library) ViennaRNA: ViennaRNA: The ViennaRNA Package consists of a C code library and several ViennaRNA: stand-alone programs for the prediction and comparison of RNA ViennaRNA: secondary structures. ViennaRNA: -ViennaRNA: Reference: Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafe +ViennaRNA: Reference: Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafe ViennaRNA: H, Flamm C, Stadler PF, Hofacker IL. ViennaRNA Package 2.0 ViennaRNA: Algorithms Mol. Biol., 6:1 26, 2011, doi:10.1186/1748-7188-6-26 ViennaRNA: Home: https://www.tbi.univie.ac.at/RNA |