academic/ViennaRNA: Update script.

Enable RNAxplorer, needs setting which blas is used to compile
lapack(e), see README and ViennaRNA.SlackBuild

Signed-off-by: Andrew Clemons <andrew.clemons@gmail.com>

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

5 files changed, 36 insertions, 15 deletions

diff --git a/academic/ViennaRNA/README b/academic/ViennaRNA/README
index a82c7160b2..69c7211233 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
@@ -27,7 +36,7 @@ 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
@@ -49,6 +58,6 @@ 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:
+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 b7d0dfc94f..1dea452cba 100644
--- a/academic/ViennaRNA/ViennaRNA.SlackBuild
+++ b/academic/ViennaRNA/ViennaRNA.SlackBuild
@@ -26,10 +26,16 @@ cd $(dirname $0) ; CWD=$(pwd)
 
 PRGNAM=ViennaRNA
 VERSION=${VERSION:-2.6.3}
-BUILD=${BUILD:-1}
+BUILD=${BUILD:-2}
 TAG=${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 ;;
@@ -101,15 +107,12 @@ find -L . \
 # for Z-score filtering via statically linked libsvm:
 # - SVM Z-score filter in RNALfold
 # - GNU Scientific Library for RNApvmin
-# RNAxplorer blocks configuration despite intalling dependencies lapacke and lapack, so ignore it
-# https://github.com/ViennaRNA/ViennaRNA/issues/206
-rnaxplorer=""    ; [ "${RNAXPLORER:-no}" != "yes" ]     && rnaxplorer="--without-rnaxplorer"
-# everything else is enabled
+# everything is enabled here
 cluster=""       ; [ "${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
@@ -131,12 +134,9 @@ CXXFLAGS="$SLKCFLAGS" \
   --mandir=/usr/man \
   --docdir=/usr/doc/$PRGNAM-$VERSION \
   --build=$ARCH-slackware-linux \
+  --with-blas=$BLAS \
   --with-python2=no \
   --with-doc=no \
-  $rnaxplorer \
-  $cluster \
-  $kinwalker \
-  $forester \
   $cluster \
   $kinwalker \
   $forester \
@@ -175,7 +175,7 @@ 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
 
@@ -199,7 +199,7 @@ 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
 
@@ -207,6 +207,8 @@ 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 c3292c1a04..2c05f2df00 100644
--- a/academic/ViennaRNA/ViennaRNA.info
+++ b/academic/ViennaRNA/ViennaRNA.info
@@ -5,6 +5,6 @@ DOWNLOAD="UNSUPPORTED"
 MD5SUM=""
 DOWNLOAD_x86_64="https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_6_x/ViennaRNA-2.6.3.tar.gz"
 MD5SUM_x86_64="405b8126efc1dd8f52bfc984d9171c9e"
-REQUIRES=""
+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