diff options
| -rw-r--r-- | academic/staden/README | 9 | ||||
| -rw-r--r-- | academic/staden/staden.SlackBuild | 93 | ||||
| -rw-r--r-- | academic/staden/staden.info | 14 |
3 files changed, 23 insertions, 93 deletions
diff --git a/academic/staden/README b/academic/staden/README index 26b87b4c05f5a..0d8a67c590563 100644 --- a/academic/staden/README +++ b/academic/staden/README @@ -18,12 +18,3 @@ TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF For more information and citing, visit Staden's web page and check the "References" file in the documentation. - -Notes: -1) You should run the SlackBuild in real root environment (su -)! -2) Make sure you have Emacs and Tetex installed at build time. -3) Although unsupported at the moment, SPIN can provide a GUI for the - EMBOSS suite programs. If you want to give it a try, run as root - "create_emboss_files" (EMBOSS should be installed, of course). This - generates some files in /usr/share/staden/tcl/spin_emboss/acdtcl, - so remember to manually clean them if you later uninstall staden. diff --git a/academic/staden/staden.SlackBuild b/academic/staden/staden.SlackBuild index cb3ee341df30e..3c132c0b6dd2b 100644 --- a/academic/staden/staden.SlackBuild +++ b/academic/staden/staden.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for staden -# Copyright 2011-2012 Petar Petrov, ppetrov@paju.oulu.fi +# Copyright 2011-2014 Petar Petrov, petar.petrov@student.oulu.fi # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,8 +23,8 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=staden -VERSION=${VERSION:-2.0.0b9} -BUILD=${BUILD:-3} +VERSION=${VERSION:-2.0.0b10} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -35,9 +35,7 @@ if [ -z "$ARCH" ]; then esac fi -SLKTCL=tcl8.6.1 # Slackware 14.1 sources for TCL -SLKTK=tk8.6.1 # Slackware 14.1 sources for TK -TKLIB=tklib0.5 # Folder name of TKLIB +TKLIB=tklib0.5 # Folder name of TKLIB CWD=$(pwd) TMP=${TMP:-/tmp/SBo} @@ -63,51 +61,19 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -mkdir $PRGNAM-$VERSION -cd $PRGNAM-$VERSION +rm -rf $PRGNAM-$VERSION-src tar xvf $CWD/$PRGNAM-$VERSION-src.tar.gz -tar xvf $CWD/${PRGNAM}_doc-$VERSION-src.tar.gz - -# The sources of TCL and TK are expected to be in /tmp at build time, -# so we unpack them in the build directory and create symlinks in /tmp. -rm -f /tmp/$SLKTCL -rm -f /tmp/$SLKTK -tar xvf $CWD/$SLKTCL-src.tar.xz -tar xvf $CWD/$SLKTK-src.tar.xz -ln -s $TMP/$PRGNAM-$VERSION/$SLKTCL /tmp/$SLKTCL -ln -s $TMP/$PRGNAM-$VERSION/$SLKTK /tmp/$SLKTK - -chown -R root:root $PRGNAM-$VERSION-src ${PRGNAM}_doc-$VERSION-src -find $PRGNAM-$VERSION-src ${PRGNAM}_doc-$VERSION-src \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; - cd $PRGNAM-$VERSION-src - -# On Slackware64, the components of staden (like GAP4, GAP5, PREGAP4, -# SPIN, TREV) will not run, as they still expect their libraries to be -# in /usr/lib not /usr/lib64. Let's correct the libraries path. +chown -R root:root . +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 {} \; + +# Make sure libraries path is correct. sed -i "s:$STADENROOT/lib:$STADENROOT/lib${LIBDIRSUFFIX}:g" \ - global.mk staden.profile copy_reads/copy_reads gap4/gap4 gap5/gap5 \ - gap5/gap5_consensus gap5/gap5_export gap5/tg_index gap5/tg_view \ - prefinish/finish_sanger prefinish/prefinish pregap4/pregap4 spin/spin \ - spin_emboss/create_emboss_files trev/trev - -# Point to the right place of the EMBOSS .acd and data files. This is -# needed if the "create_emboss_files" script is run after install. -sed -i "133 c set acd_dir /usr/share/EMBOSS/acd" spin_emboss/create_emboss_files.tcl -sed -i "73 a EMBOSS_DATA=/usr/share/EMBOSS/data; export EMBOSS_DATA" spin/spin - -# Correct the path where staden components look for their manual. -sed -i "s:/share/doc/staden/manual:/doc/$PRGNAM-$VERSION/manual:" tk_utils/help_config - -# These fixes are from Arch linux AUR -# http://aur.archlinux.org/packages/st/staden/PKGBUILD -sed -i 's:-DSVN_VERSION=$(SVNVERS)::' system.mk.in -sed -i "s/gzFile\ \*gz/gzFile\ gz/" gap5/zfio.h + global.mk staden.profile CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -124,41 +90,20 @@ CXXFLAGS="$SLKCFLAGS" \ make make install DESTDIR=$PKG -# Build documentation. In the process, texi2dvi looks for tex and -# that's why the SlackBuild should be run as real root (su -). -# ## (or just source /etc/profile ) --rworkman -cd $TMP/$PRGNAM-$VERSION/${PRGNAM}_doc-$VERSION-src - -# Fix the doc and man pages paths -sed "s:{datarootdir}/doc/staden:{prefix}/doc/$PRGNAM-$VERSION:" -i Makefile -sed "s:{datarootdir}/man:{prefix}/man:" -i Makefile - -# Remove this, or there will be an error at the "make install" line. -rm -rf i/i - -# Generate documentation. If you want it in the US letter format, -# change the next line to "make unix PAPER=us". -make unix -make install DESTDIR=$PKG - -# Now that we're done building, let's remove those symlinks from earlier... -rm -f /tmp/$SLKTCL /tmp/$SLKTK - -# This is empty +# These are empty rm -rf $PKG/usr/share/doc +rm -rf $PKG/usr/man 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 - mkdir -p $PKG/usr/share/{applications,pixmaps} cp $CWD/desktop/*.desktop $PKG/usr/share/applications cp $CWD/desktop/*.png $PKG/usr/share/pixmaps -cd ../$PRGNAM-$VERSION-src -cp -a ChangeLog NEWS README.build $PKG/usr/doc/$PRGNAM-$VERSION +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a ChangeLog LICENCE.txt NEWS README.build \ + $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References diff --git a/academic/staden/staden.info b/academic/staden/staden.info index d3a31aedebcf4..15238270ef562 100644 --- a/academic/staden/staden.info +++ b/academic/staden/staden.info @@ -1,16 +1,10 @@ PRGNAM="staden" -VERSION="2.0.0b9" +VERSION="2.0.0b10" HOMEPAGE="http://staden.sourceforge.net/" -DOWNLOAD="http://sourceforge.net/projects/staden/files/staden/2.0.0b9/staden-2.0.0b9-src.tar.gz \ - http://sourceforge.net/projects/staden/files/staden/2.0.0b9/staden_doc-2.0.0b9-src.tar.gz \ - http://slackware.osuosl.org/slackware-14.1/source/tcl/tcl/tcl8.6.1-src.tar.xz \ - http://slackware.osuosl.org/slackware-14.1/source/tcl/tk/tk8.6.1-src.tar.xz" -MD5SUM="94dc304b00d18b95f783136c9ffd934f \ - 730b433d8344624925b662ec37ac0804 \ - 59d2b6a9ac7dacee4c2f61b79f99b300 \ - 2937055d4d0693271f7485de94c761d2" +DOWNLOAD="http://sourceforge.net/projects/staden/files/staden/2.0.0b10/staden-2.0.0b10-src.tar.gz" +MD5SUM="81ad0b840253774e41d3089fca7af688" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="io_lib tklib" MAINTAINER="Petar Petrov" -EMAIL="ppetrov@paju.oulu.fi" +EMAIL="petar.petrov@student.oulu.fi" |