diff options
Diffstat (limited to 'academic/ViennaRNA')
| -rw-r--r-- | academic/ViennaRNA/README | 36 | ||||
| -rw-r--r-- | academic/ViennaRNA/ViennaRNA.SlackBuild | 46 | ||||
| -rw-r--r-- | academic/ViennaRNA/ViennaRNA.info | 8 | ||||
| -rw-r--r-- | academic/ViennaRNA/swig4.patch | 203 |
4 files changed, 53 insertions, 240 deletions
diff --git a/academic/ViennaRNA/README b/academic/ViennaRNA/README index a8fb799e79..6ad531d628 100644 --- a/academic/ViennaRNA/README +++ b/academic/ViennaRNA/README @@ -1,8 +1,21 @@ # ViennaRNA Package -A C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. +A C code library and several stand-alone programs for the prediction +and comparison of RNA secondary structures. -Amongst other things, our implementations allow you to: +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: + +https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/index.html +(or unpacked from the src: $PRGNAM-$VERSION/doc/html/) +https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/RNAlib-$VERSION.pdf +(or unpacked from the src: $PRGNAM-$VERSION/doc/RNAlib-$VERSION.pdf) + +Amongst other things, the ViennRNA implementations allow you to: - predict minimum free energy secondary structures - calculate the partition function for the ensemble of structures @@ -15,9 +28,15 @@ Amongst other things, our implementations allow you to: - compare two secondary structures - predict hybridization structures of two RNA molecules -The package includes `Perl 5`, `Python 2`, and `Python 3` modules that give +The package includes `Perl 5` and `Python 3` modules that give access to almost all functions of the C library from within the respective -scripting languages. +scripting languages. For this reason, python3 is a dependency + +The `Python 2` module can be built as well, or instead of the one for `Python 3`; +just edit the SlackBuild or run it by setting build options PYTHON=yes PYTHON3=no. +(e.g. in sbopkg or run it from the commandline -within the directory containing +the SlackBuild script and downloaded source archive- as: +`PYTHON=yes PYTHON3=no ./ViennaRNA.SlackBuild`) There is also a set of programs for analyzing sequence and distance data using split decomposition, statistical geometry, and cluster methods. @@ -27,15 +46,6 @@ The code very rarely uses static arrays, and all programs should work for sequences up to a length of 32,700 (if you have huge amounts of memory that is). -For those who wish to link the Vienna package their own C, perl or python programs, -the RNAlib Reference Manual can be assessed at: - -https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/index.html - -or downloaded from: - -https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/RNAlib-$VERSION.pdf - For further info see: https://www.tbi.univie.ac.at/RNA/documentation.html diff --git a/academic/ViennaRNA/ViennaRNA.SlackBuild b/academic/ViennaRNA/ViennaRNA.SlackBuild index 9de92bfa6e..5b8a1882a2 100644 --- a/academic/ViennaRNA/ViennaRNA.SlackBuild +++ b/academic/ViennaRNA/ViennaRNA.SlackBuild @@ -23,13 +23,13 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=ViennaRNA -VERSION=${VERSION:-2.4.12} +VERSION=${VERSION:-2.4.13} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -40,8 +40,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -63,16 +63,11 @@ rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . -find . \ - \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - -patch -p 1 < $CWD/swig4.patch - -#needed to make patches compile -autoreconf +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # You can configure some ViennaRNA features that are (not) compiled by default. # See the README.md for details. You can enable/disable a these features by @@ -107,7 +102,7 @@ forester="" ; [ "${FORESTER:-yes}" != "yes" ] && forester="--without-fo kinfold="" ; [ "${KINFOLD:-yes}" != "yes" ] && kinwalk="--without-kinfold" rnalocmin="" ; [ "${RNALOCMIN:-yes}" != "yes" ] && rnalocmin="--without-rnalocmin" perl="" ; [ "${PERL:-yes}" != "yes" ] && perl="--without-perl" -python="" ; [ "${PYTHON:-yes}" != "yes" ] && python="--without-python" + python3="" ; [ "${PYTHON3:-yes}" != "yes" ] && python3="--without-python3" swig="" ; [ "${SWIG:-yes}" != "yes" ] && swig="--without-swig" simd="" ; [ "${SIMD:-yes}" != "yes" ] && simd="--disable-simd" @@ -116,6 +111,8 @@ openmp="" ; [ "${OPENMP:-yes}" != "yes" ] && openmp="--disable-openm pthreads="" ; [ "${PTHREADS:-yes}" != "yes" ] && pthreads="--disable-pthreads" svm="" ; [ "${SVM:-yes}" != "yes" ] && svm="--without-svm" gsl="" ; [ "${GSL:-yes}" != "yes" ] && gsl="--without-gsl" +# Default to python3 (above) only; +python="" ; [ "${PYTHON:-no}" != "yes" ] && python="--without-python" CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -149,12 +146,14 @@ cd misc make install DESTDIR=$PKG cd .. +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + # cleanup after dirty install ... -# install -dm755 $PKG/usr/bin/vendor_perl for perlscript in $PKG/usr/share/ViennaRNA/bin/*.pl ; do -# mv "$perlscript" "$PKG/usr/bin/vendor_perl/" mv "$perlscript" "$PKG/usr/bin/" done +rm -r $PKG/usr/share/ViennaRNA/bin # no need for that file it is outdated anyway rm $PKG/usr/share/info/dir @@ -162,9 +161,6 @@ rm $PKG/usr/share/info/dir #gzip info file gzip -9 $PKG/usr/share/info/*.info -find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ - | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true - find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done @@ -174,6 +170,16 @@ find $PKG -name perllocal.pod \ | xargs rm -f mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION + +#keep help and RNAlib-${VERSION} in src +if [[ -d $PKG/usr/doc/$PRGNAM-$VERSION/html ]]; then + rm -r $PKG/usr/doc/$PRGNAM-$VERSION/html +fi + +if [[ -e $PKG/usr/doc/$PRGNAM-$VERSION/RNAlib-$VERSION.pdf ]]; then + rm $PKG/usr/doc/$PRGNAM-$VERSION/RNAlib-$VERSION.pdf +fi + cp -a \ NEWS README.md AUTHORS COPYING THANKS INSTALL CHANGELOG.md license.txt \ $PKG/usr/doc/$PRGNAM-$VERSION diff --git a/academic/ViennaRNA/ViennaRNA.info b/academic/ViennaRNA/ViennaRNA.info index 1432a46dc1..5e7cdc20e0 100644 --- a/academic/ViennaRNA/ViennaRNA.info +++ b/academic/ViennaRNA/ViennaRNA.info @@ -1,10 +1,10 @@ PRGNAM="ViennaRNA" -VERSION="2.4.12" +VERSION="2.4.13" HOMEPAGE="https://www.tbi.univie.ac.at/RNA" -DOWNLOAD="https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.12.tar.gz" -MD5SUM="db37ca5c863375d61488e6d7248c7176" +DOWNLOAD="https://github.com/ViennaRNA/ViennaRNA/releases/download/v2.4.13/ViennaRNA-2.4.13.tar.gz" +MD5SUM="bd52c7ae189040b4b3cd328da5490b99" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="grace gri" +REQUIRES="python3 gri" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" diff --git a/academic/ViennaRNA/swig4.patch b/academic/ViennaRNA/swig4.patch deleted file mode 100644 index 88df2eb933..0000000000 --- a/academic/ViennaRNA/swig4.patch +++ /dev/null @@ -1,203 +0,0 @@ -commit c8a867dc017f58a4ffbfb2d3d976506947e5d9d6 -Author: Ronny Lorenz <ronny@tbi.univie.ac.at> -Date: Mon May 13 08:22:42 2019 +0200 - - SWIG: Fix install for wrappers generated by swig 4 - - - We now default to install _RNA.*so files for Python2/3 into the RNA/ - subdirectory. This seems necessary to avoid problems when importing - the RNA package, where the underlying loader changed from swig 3 to - swig 4. - - We also require swig 3.0.0 or later from now on to generate the - wrapper code, and we drop the -modern flag - -diff --git a/interfaces/Python/Makefile.am b/interfaces/Python/Makefile.am -index df279501..41be4c08 100644 ---- a/interfaces/Python/Makefile.am -+++ b/interfaces/Python/Makefile.am -@@ -16,9 +16,8 @@ INTERFACE_FILES = $(SWIG_src) \ - $(LANG_SPECIFIC_INTERFACE_FILES) - - pkgpy2execdir = $(py2execdir)/RNA --pkgpy2cmoddir = $(py2execdir) - --pkgpy2cmod_LTLIBRARIES = _RNA.la -+pkgpy2exec_LTLIBRARIES = _RNA.la - pkgpy2exec_DATA = RNA/__init__.py - - _RNA_la_SOURCES = $(INTERFACE_FILES) \ -@@ -73,7 +72,7 @@ $(SWIG_wrapper): $(SWIG_src) $(INTERFACE_FILES) - $(swig_verbose)$(SWIG) -I$(top_srcdir)/src \ - -I$(srcdir) -I$(builddir) \ - $(RNA_CPPFLAGS) \ -- -python -modern -c++ \ -+ -python -c++ \ - -o $(SWIG_wrapper) \ - $(SWIG_main_src) - -@@ -87,27 +86,33 @@ RNA/__init__.py: $(SWIG_module_name).py - $(AM_V_GEN)( test -d RNA || $(MKDIR_P) RNA ) && \ - cp `test -f RNA.py || echo '$(srcdir)/'`RNA.py RNA/__init__.py - --_RNA$(PYTHON2_SO): _RNA.la -- $(AM_V_GEN)( $(LIBTOOL) --config > libtoolconfig.tmp ) && \ -- ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON2_SO) . ) && \ -+RNA/_RNA$(PYTHON2_SO): _RNA.la -+ $(AM_V_GEN)( test -d RNA || $(MKDIR_P) RNA ) && \ -+ ( $(LIBTOOL) --config > libtoolconfig.tmp ) && \ -+ ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON2_SO) RNA ) && \ - rm -f libtoolconfig.tmp - --all-local: _RNA$(PYTHON2_SO) -+CLEANFILES = \ -+ RNA/_RNA$(PYTHON2_SO) \ -+ RNA/__init__.py \ -+ RNA/__init__.pyc -+ -+all-local: RNA/_RNA$(PYTHON2_SO) - - clean-local: -- -rm -rf RNA _RNA$(PYTHON2_SO) -+ -rm -rf RNA - - # Remove the .la file - RNA.la is never linked against (it's a module) - # and Python doesn't use libltdl. Note that the library gets installed by - # install-data, so that's where we need to hook. - install-data-hook: -- rm -f $(DESTDIR)$(pkgpy2cmoddir)/_RNA.la -+ rm -f $(DESTDIR)$(pkgpy2execdir)/_RNA.la - - # Because we don't install the .la file, "make uninstall" doesn't work and - # we need to remove the file ourselves. - uninstall-local: -- eval `grep '^dlname=' $(pkgpy2cmod_LTLIBRARIES)` ; \ -- rm -f $(DESTDIR)$(pkgpy2cmoddir)/"$$dlname" -+ eval `grep '^dlname=' $(pkgpy2exec_LTLIBRARIES)` ; \ -+ rm -f $(DESTDIR)$(pkgpy2execdir)/"$$dlname" - - ## remove all generated content - maintainer-clean-local: -diff --git a/interfaces/Python3/Makefile.am b/interfaces/Python3/Makefile.am -index de9b049e..67824a99 100644 ---- a/interfaces/Python3/Makefile.am -+++ b/interfaces/Python3/Makefile.am -@@ -17,10 +17,9 @@ INTERFACE_FILES = $(SWIG_src) \ - $(LANG_SPECIFIC_INTERFACE_FILES) - - pkgpyexecdir = $(py3execdir)/RNA --pkgpycmoddir = $(py3execdir) - pkgpycachedir = $(pkgpyexecdir)/__pycache__ - --pkgpycmod_LTLIBRARIES = _RNA.la -+pkgpyexec_LTLIBRARIES = _RNA.la - pkgpyexec_DATA = RNA/__init__.py - pkgpycache_DATA = RNA/__pycache__/__init__.@PYTHON3_CACHE_TAG@.pyc \ - RNA/__pycache__/__init__.@PYTHON3_CACHE_OPT1_EXT@ -@@ -75,7 +74,7 @@ $(SWIG_wrapper): $(SWIG_src) $(INTERFACE_FILES) - -I$(srcdir) -I$(builddir) \ - -DPY3 \ - $(RNA_CPPFLAGS) \ -- -python -modern -py3 -c++ \ -+ -python -py3 -c++ \ - -o $(SWIG_wrapper) \ - $(SWIG_main_src) - -@@ -91,42 +90,43 @@ RNA/__init__.py: $(SWIG_module_name).py - - # We "import _RNA" first so that if we fail to import the glue library - # we don't generate a broken .pyc or .pyo. --RNA/__pycache__/__init__.@PYTHON3_CACHE_TAG@.pyc: RNA/__init__.py _RNA$(PYTHON3_SO) -+RNA/__pycache__/__init__.@PYTHON3_CACHE_TAG@.pyc: RNA/__init__.py RNA/_RNA$(PYTHON3_SO) - $(AM_V_GEN)( PYTHONPATH="RNA:$$PYTHONPATH" $(PYTHON3) -c "import _RNA" ; \ - PYTHONPATH=".:$$PYTHONPATH" $(PYTHON3) -c "import RNA" ) - --RNA/__pycache__/__init__.@PYTHON3_CACHE_OPT1_EXT@: RNA/__init__.py _RNA$(PYTHON3_SO) -+RNA/__pycache__/__init__.@PYTHON3_CACHE_OPT1_EXT@: RNA/__init__.py RNA/_RNA$(PYTHON3_SO) - $(AM_V_GEN)( PYTHONPATH="RNA:$$PYTHONPATH" $(PYTHON3) -O -c "import _RNA" ; \ - PYTHONPATH=".:$$PYTHONPATH" $(PYTHON3) -O -c "import RNA" ) - --_RNA$(PYTHON3_SO): _RNA.la -- $(AM_V_GEN)( $(LIBTOOL) --config > libtoolconfig.tmp ) && \ -- ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON3_SO) . ) && \ -+RNA/_RNA$(PYTHON3_SO): _RNA.la -+ $(AM_V_GEN)( test -d RNA || $(MKDIR_P) RNA ) && \ -+ ( $(LIBTOOL) --config > libtoolconfig.tmp ) && \ -+ ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON3_SO) RNA ) && \ - rm -f libtoolconfig.tmp - - CLEANFILES = \ -- _RNA$(PYTHON3_SO) \ -+ RNA/_RNA$(PYTHON3_SO) \ - RNA/__init__.py \ - RNA/__pycache__/__init__.@PYTHON3_CACHE_TAG@.pyc \ - RNA/__pycache__/__init__.@PYTHON3_CACHE_OPT1_EXT@\ - $(srcdir)/*.pyc - --all-local: _RNA$(PYTHON3_SO) -+all-local: RNA/_RNA$(PYTHON3_SO) - - clean-local: -- -rm -rf RNA _RNA$(PYTHON3_SO) -+ -rm -rf RNA - - # Remove the .la file - RNA.la is never linked against (it's a module) - # and Python doesn't use libltdl. Note that the library gets installed by - # install-data, so that's where we need to hook. - install-data-hook: -- rm -f $(DESTDIR)$(pkgpycmoddir)/_RNA.la -+ rm -f $(DESTDIR)$(pkgpyexecdir)/_RNA.la - - # Because we don't install the .la file, "make uninstall" doesn't work and - # we need to remove the file ourselves. - uninstall-local: -- eval `grep '^dlname=' $(pkgpycmod_LTLIBRARIES)` ; \ -- rm -f $(DESTDIR)$(pkgpycmoddir)/"$$dlname" -+ eval `grep '^dlname=' $(pkgpyexec_LTLIBRARIES)` ; \ -+ rm -f $(DESTDIR)$(pkgpyexecdir)/"$$dlname" - - ## remove all generated content - maintainer-clean-local: -diff --git a/interfaces/RNA.i b/interfaces/RNA.i -index fb2260d6..6ae86641 100644 ---- a/interfaces/RNA.i -+++ b/interfaces/RNA.i -@@ -1,4 +1,9 @@ -+#ifdef SWIGPYTHON -+%module(moduleimport="from . import _RNA") RNA -+#else - %module RNA -+#endif -+ - //%pragma(perl5) modulecode="@EXPORT=qw(fold);" - %pragma(perl5) include="RNA.pod" - -diff --git a/m4/ac_rna_swig.m4 b/m4/ac_rna_swig.m4 -index 98583bed..29ea398f 100644 ---- a/m4/ac_rna_swig.m4 -+++ b/m4/ac_rna_swig.m4 -@@ -9,13 +9,12 @@ AC_DEFUN([RNA_ENABLE_SWIG_INTERFACES],[ - - AS_IF([test "x$with_swig" != "xno"],[ - wants_swig="yes" -- AX_PKG_SWIG(2.0.0, [has_swig="yes"], [has_swig="no"]) -+ AX_PKG_SWIG(3.0.0, [has_swig="yes"], [has_swig="no"]) - ],[ - wants_swig="no" - ]) - - AM_CONDITIONAL(HAS_SWIG, test "x$has_swig" != "xno") -- - RNA_ENABLE_SWIG_PERL - RNA_ENABLE_SWIG_PYTHON - RNA_ENABLE_SWIG_PYTHON3 -@@ -55,10 +54,6 @@ AC_DEFUN([RNA_ENABLE_SWIG_PERL],[ - AC_MSG_ERROR([Perl is required to build.]) - [enable_perl_status="Perl is required to build."] - fi --# AX_PERL_EXT_FLAGS([PERLXS_CFLAGS], [PERLXS_LDFLAGS]) --# AX_PERL_EXT_LINK_CHECK([with_perl]) --# AC_SUBST([PERLXS_CFLAGS]) --# AC_SUBST([PERLXS_LDFLAGS]) - ]) - - # prepare all files for perl interface |