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Diffstat (limited to 'academic/ViennaRNA/README')
| -rw-r--r-- | academic/ViennaRNA/README | 41 |
1 files changed, 19 insertions, 22 deletions
diff --git a/academic/ViennaRNA/README b/academic/ViennaRNA/README index 6ad531d628..4807f340a8 100644 --- a/academic/ViennaRNA/README +++ b/academic/ViennaRNA/README @@ -3,12 +3,22 @@ A C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. +A recent addition, RNAxplorer, requires lapacke (which requires +lapack that depends on a version of blas). During configuration the +step for RNAxplorer stalls (on missing lapack) because it does not +find the version of blas that has been used for compiling lapack +(see https://github.com/ViennaRNA/ViennaRNA/issues/206). +An extra variable ($BLAS) in the SlackBuild sets openblas as the +version of blas used for lapack(e). Please, adjust $BLAS to the blas +used on your system. + A tutorial (see /usr/doc/$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/) @@ -22,30 +32,17 @@ 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 +- 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 -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`) - -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. - -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 package includes `Perl` and `Python 3` modules that give access +to almost all functions of the C library from within the respective +scripting languages. -For further info see: +For further/most recent info see: https://www.tbi.univie.ac.at/RNA/documentation.html |