diff options
Diffstat (limited to 'academic/ViennaRNA')
| -rw-r--r-- | academic/ViennaRNA/README | 32 | ||||
| -rw-r--r-- | academic/ViennaRNA/ViennaRNA.SlackBuild | 30 | ||||
| -rw-r--r-- | academic/ViennaRNA/ViennaRNA.info | 12 | ||||
| -rw-r--r-- | academic/ViennaRNA/doinst.sh | 4 | ||||
| -rw-r--r-- | academic/ViennaRNA/douninst.sh | 6 |
5 files changed, 45 insertions, 39 deletions
diff --git a/academic/ViennaRNA/README b/academic/ViennaRNA/README index a82c7160b2..4807f340a8 100644 --- a/academic/ViennaRNA/README +++ b/academic/ViennaRNA/README @@ -3,6 +3,15 @@ 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 @@ -27,28 +36,13 @@ Amongst other things, the ViennRNA implementations allow you to: 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 +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 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). +scripting languages. -For further info see: +For further/most recent info see: https://www.tbi.univie.ac.at/RNA/documentation.html diff --git a/academic/ViennaRNA/ViennaRNA.SlackBuild b/academic/ViennaRNA/ViennaRNA.SlackBuild index 9d6da8902e..42ae76bbd7 100644 --- a/academic/ViennaRNA/ViennaRNA.SlackBuild +++ b/academic/ViennaRNA/ViennaRNA.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for ViennaRNA -# Copyright 2018-2022 Rob van Nues +# Copyright 2018-2023 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,11 +25,17 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=ViennaRNA -VERSION=${VERSION:-2.5.1} +VERSION=${VERSION:-2.6.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} +# RNAxplorer requires lapacke (which requires lapack that requires blas) +# but cannot see what blas is used for compiling lapack +# please adjust $BLAS to the blas installed on your system +BLAS=${BLAS:-openblas} + + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -38,9 +44,6 @@ if [ -z "$ARCH" ]; then esac fi -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" exit 0 @@ -92,8 +95,7 @@ find -L . \ # - RNAlocmin # - Swig (all scripting interfaces) # - Perl interface -# - Python interface -# - Python 3 interface +# - Python 3 interface (= Python interface) # - Streaming SIMD Extension support # in the case of run time/ make/ or configure problems try turning off: # - Link Time Optimization (LTO) @@ -104,12 +106,12 @@ find -L . \ # for Z-score filtering via statically linked libsvm: # - SVM Z-score filter in RNALfold # - GNU Scientific Library for RNApvmin - +# everything is enabled here cluster="" ; [ "${CLUSTER:-yes}" != "no" ] && cluster="--with-cluster" kinwalker="" ; [ "${KINWALKER:-yes}" != "no" ] && kinwalker="--with-kinwalker" # Default enabled features: forester="" ; [ "${FORESTER:-yes}" != "no" ] && forester="--with-forester" -kinfold="" ; [ "${KINFOLD:-yes}" != "no" ] && kinwalk="--with-kinfold" +kinfold="" ; [ "${KINFOLD:-yes}" != "no" ] && kinfold="--with-kinfold" rnalocmin="" ; [ "${RNALOCMIN:-yes}" != "no" ] && rnalocmin="--with-rnalocmin" perl="" ; [ "${PERL:-yes}" != "no" ] && perl="--with-perl" # python = python3 @@ -131,14 +133,12 @@ CXXFLAGS="$SLKCFLAGS" \ --mandir=/usr/man \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --build=$ARCH-slackware-linux \ + --with-blas=$BLAS \ --with-python2=no \ --with-doc=no \ $cluster \ $kinwalker \ $forester \ - $cluster \ - $kinwalker \ - $forester \ $kinfold \ $rnalocmin \ $perl \ @@ -174,7 +174,7 @@ rm -r $PKG/usr/share/ViennaRNA/bin mkdir $PKG/usr/info/ rm $PKG/usr/share/info/dir #gzip and move info file -gzip -9 $PKG/usr/share/info/*.info +gzip -9 $PKG/usr/share/info/*.info* mv $PKG/usr/share/info/*.info* $PKG/usr/info/ rmdir $PKG/usr/share/info @@ -198,7 +198,7 @@ if [[ -e $PKG/usr/doc/$PRGNAM-$VERSION/RNAlib-$VERSION.pdf ]]; then fi cp -a \ - NEWS README.md AUTHORS COPYING THANKS INSTALL CHANGELOG.md license.txt \ + NEWS README.md AUTHORS COPYING THANKS CHANGELOG.md license.txt \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -206,6 +206,8 @@ rm -f $PKG/usr/lib*/*.la mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh +cat $CWD/douninst.sh > $PKG/install/douninst.sh cd $PKG /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/ViennaRNA/ViennaRNA.info b/academic/ViennaRNA/ViennaRNA.info index eeb3430e3b..b871a31ccc 100644 --- a/academic/ViennaRNA/ViennaRNA.info +++ b/academic/ViennaRNA/ViennaRNA.info @@ -1,10 +1,10 @@ PRGNAM="ViennaRNA" -VERSION="2.5.1" +VERSION="2.6.4" HOMEPAGE="https://www.tbi.univie.ac.at/RNA" -DOWNLOAD="https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_5_x/ViennaRNA-2.5.1.tar.gz" -MD5SUM="25abee6dc24b863e50d44b154357b9c7" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_6_x/ViennaRNA-2.6.4.tar.gz" +MD5SUM_x86_64="6d8fd8ffe44d70399bff220f709a2b55" +REQUIRES="lapacke" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/ViennaRNA/doinst.sh b/academic/ViennaRNA/doinst.sh new file mode 100644 index 0000000000..fe39c0a9d2 --- /dev/null +++ b/academic/ViennaRNA/doinst.sh @@ -0,0 +1,4 @@ +if [ -x /usr/bin/install-info ]; then + /usr/bin/install-info --info-dir=usr/info usr/info/RNAlib.info.gz 1> /dev/null 2>&1 +fi + diff --git a/academic/ViennaRNA/douninst.sh b/academic/ViennaRNA/douninst.sh new file mode 100644 index 0000000000..1bef502028 --- /dev/null +++ b/academic/ViennaRNA/douninst.sh @@ -0,0 +1,6 @@ +if [ -x /usr/bin/install-info -a -d usr/info ]; then + ( cd usr/info + rm -f dir + for i in *.info*; do /usr/bin/install-info $i dir 2>/dev/null; done + ) +fi |