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academic/staden: Updated for version 2.0.0b10.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Erik Hanson
parent
234ecffbe2
commit
9d8a8a88ef
3 changed files with 22 additions and 92 deletions
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@ -18,12 +18,3 @@ TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF
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For more information and citing, visit Staden's web page and check the
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"References" file in the documentation.
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Notes:
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1) You should run the SlackBuild in real root environment (su -)!
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2) Make sure you have Emacs and Tetex installed at build time.
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3) Although unsupported at the moment, SPIN can provide a GUI for the
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EMBOSS suite programs. If you want to give it a try, run as root
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"create_emboss_files" (EMBOSS should be installed, of course). This
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generates some files in /usr/share/staden/tcl/spin_emboss/acdtcl,
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so remember to manually clean them if you later uninstall staden.
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@ -2,7 +2,7 @@
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# Slackware build script for staden
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# Copyright 2011-2012 Petar Petrov, ppetrov@paju.oulu.fi
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# Copyright 2011-2014 Petar Petrov, petar.petrov@student.oulu.fi
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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@ -23,8 +23,8 @@
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=staden
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VERSION=${VERSION:-2.0.0b9}
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BUILD=${BUILD:-3}
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VERSION=${VERSION:-2.0.0b10}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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@ -35,9 +35,7 @@ if [ -z "$ARCH" ]; then
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esac
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fi
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SLKTCL=tcl8.6.1 # Slackware 14.1 sources for TCL
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SLKTK=tk8.6.1 # Slackware 14.1 sources for TK
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TKLIB=tklib0.5 # Folder name of TKLIB
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TKLIB=tklib0.5 # Folder name of TKLIB
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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@ -63,51 +61,19 @@ set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM-$VERSION
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mkdir $PRGNAM-$VERSION
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cd $PRGNAM-$VERSION
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rm -rf $PRGNAM-$VERSION-src
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tar xvf $CWD/$PRGNAM-$VERSION-src.tar.gz
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tar xvf $CWD/${PRGNAM}_doc-$VERSION-src.tar.gz
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# The sources of TCL and TK are expected to be in /tmp at build time,
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# so we unpack them in the build directory and create symlinks in /tmp.
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rm -f /tmp/$SLKTCL
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rm -f /tmp/$SLKTK
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tar xvf $CWD/$SLKTCL-src.tar.xz
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tar xvf $CWD/$SLKTK-src.tar.xz
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ln -s $TMP/$PRGNAM-$VERSION/$SLKTCL /tmp/$SLKTCL
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ln -s $TMP/$PRGNAM-$VERSION/$SLKTK /tmp/$SLKTK
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chown -R root:root $PRGNAM-$VERSION-src ${PRGNAM}_doc-$VERSION-src
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find $PRGNAM-$VERSION-src ${PRGNAM}_doc-$VERSION-src \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \
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-exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
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-exec chmod 644 {} \;
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cd $PRGNAM-$VERSION-src
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# On Slackware64, the components of staden (like GAP4, GAP5, PREGAP4,
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# SPIN, TREV) will not run, as they still expect their libraries to be
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# in /usr/lib not /usr/lib64. Let's correct the libraries path.
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# Make sure libraries path is correct.
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sed -i "s:$STADENROOT/lib:$STADENROOT/lib${LIBDIRSUFFIX}:g" \
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global.mk staden.profile copy_reads/copy_reads gap4/gap4 gap5/gap5 \
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gap5/gap5_consensus gap5/gap5_export gap5/tg_index gap5/tg_view \
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prefinish/finish_sanger prefinish/prefinish pregap4/pregap4 spin/spin \
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spin_emboss/create_emboss_files trev/trev
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# Point to the right place of the EMBOSS .acd and data files. This is
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# needed if the "create_emboss_files" script is run after install.
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sed -i "133 c set acd_dir /usr/share/EMBOSS/acd" spin_emboss/create_emboss_files.tcl
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sed -i "73 a EMBOSS_DATA=/usr/share/EMBOSS/data; export EMBOSS_DATA" spin/spin
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# Correct the path where staden components look for their manual.
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sed -i "s:/share/doc/staden/manual:/doc/$PRGNAM-$VERSION/manual:" tk_utils/help_config
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# These fixes are from Arch linux AUR
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# http://aur.archlinux.org/packages/st/staden/PKGBUILD
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sed -i 's:-DSVN_VERSION=$(SVNVERS)::' system.mk.in
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sed -i "s/gzFile\ \*gz/gzFile\ gz/" gap5/zfio.h
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global.mk staden.profile
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CFLAGS="$SLKCFLAGS" \
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CXXFLAGS="$SLKCFLAGS" \
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@ -124,41 +90,20 @@ CXXFLAGS="$SLKCFLAGS" \
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make
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make install DESTDIR=$PKG
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# Build documentation. In the process, texi2dvi looks for tex and
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# that's why the SlackBuild should be run as real root (su -).
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# ## (or just source /etc/profile ) --rworkman
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cd $TMP/$PRGNAM-$VERSION/${PRGNAM}_doc-$VERSION-src
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# Fix the doc and man pages paths
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sed "s:{datarootdir}/doc/staden:{prefix}/doc/$PRGNAM-$VERSION:" -i Makefile
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sed "s:{datarootdir}/man:{prefix}/man:" -i Makefile
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# Remove this, or there will be an error at the "make install" line.
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rm -rf i/i
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# Generate documentation. If you want it in the US letter format,
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# change the next line to "make unix PAPER=us".
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make unix
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make install DESTDIR=$PKG
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# Now that we're done building, let's remove those symlinks from earlier...
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rm -f /tmp/$SLKTCL /tmp/$SLKTK
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# This is empty
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# These are empty
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rm -rf $PKG/usr/share/doc
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rm -rf $PKG/usr/man
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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find $PKG/usr/man -type f -exec gzip -9 {} \;
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for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
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mkdir -p $PKG/usr/share/{applications,pixmaps}
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cp $CWD/desktop/*.desktop $PKG/usr/share/applications
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cp $CWD/desktop/*.png $PKG/usr/share/pixmaps
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cd ../$PRGNAM-$VERSION-src
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cp -a ChangeLog NEWS README.build $PKG/usr/doc/$PRGNAM-$VERSION
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a ChangeLog LICENCE.txt NEWS README.build \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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@ -1,16 +1,10 @@
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PRGNAM="staden"
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VERSION="2.0.0b9"
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VERSION="2.0.0b10"
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HOMEPAGE="http://staden.sourceforge.net/"
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DOWNLOAD="http://sourceforge.net/projects/staden/files/staden/2.0.0b9/staden-2.0.0b9-src.tar.gz \
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http://sourceforge.net/projects/staden/files/staden/2.0.0b9/staden_doc-2.0.0b9-src.tar.gz \
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http://slackware.osuosl.org/slackware-14.1/source/tcl/tcl/tcl8.6.1-src.tar.xz \
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http://slackware.osuosl.org/slackware-14.1/source/tcl/tk/tk8.6.1-src.tar.xz"
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MD5SUM="94dc304b00d18b95f783136c9ffd934f \
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730b433d8344624925b662ec37ac0804 \
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59d2b6a9ac7dacee4c2f61b79f99b300 \
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2937055d4d0693271f7485de94c761d2"
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DOWNLOAD="http://sourceforge.net/projects/staden/files/staden/2.0.0b10/staden-2.0.0b10-src.tar.gz"
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MD5SUM="81ad0b840253774e41d3089fca7af688"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="io_lib tklib"
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MAINTAINER="Petar Petrov"
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EMAIL="ppetrov@paju.oulu.fi"
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EMAIL="petar.petrov@student.oulu.fi"
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