academic/tabix: Added (Generic indexer).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
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Tabix indexes a TAB-delimited genome position file in.tab.bgz and
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creates an index file in.tab.bgz.tbi when region is absent from the
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command-line. The input data file must be position sorted and
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compressed by bgzip which has a gzip like interface. After indexing,
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tabix is able to quickly retrieve data lines overlapping regions
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specified in the format "chr:beginPos-endPos". Fast data retrieval
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also works over network if URI is given as a file name and in this
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case the index file will be downloaded if it is not present locally.
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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tabix: tabix (Generic indexer for TAB-delimited genome position files )
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tabix:
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tabix: Tabix indexes a TAB-delimited genome position file in.tab.bgz
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tabix: and creates an index file in.tab.bgz.tbi when region is absent
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tabix: from the command-line. The input data file must be position
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tabix: sorted and compressed by bgzip which has a gzip like interface.
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tabix: Tabix is able to quickly retrieve data lines overlapping regions
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tabix: specified in the format "chr:beginPos-endPos".
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tabix:
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tabix: Home: http://samtools.sourceforge.net/tabix.shtml
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tabix:
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#!/bin/sh
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# Slackware build script for tabix
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# Copyright 2013 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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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=tabix
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VERSION=${VERSION:-0.2.6}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i486 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i486" ]; then
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SLKCFLAGS="-O2 -march=i486 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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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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tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2
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cd $PRGNAM-$VERSION
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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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CFLAGS="$SLKCFLAGS" \
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CXXFLAGS="$SLKCFLAGS" \
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make
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# Install executables
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install -D -m755 tabix $PKG/usr/bin/tabix
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install -D -m755 bgzip $PKG/usr/bin/bgzip
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# Place manpage
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install -D -m644 $PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1
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# Include examples
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mkdir -p $PKG/usr/share/$PRGNAM
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cp -a example.gtf.gz example.gtf.gz.tbi $PKG/usr/share/$PRGNAM
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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 $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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ChangeLog NEWS \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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PRGNAM="tabix"
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VERSION="0.2.6"
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HOMEPAGE="http://samtools.sourceforge.net/tabix.shtml"
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DOWNLOAD="http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2"
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MD5SUM="36a61ceac2f5bed36018434282bbcc5d"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES=""
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MAINTAINER="Petar Petrov"
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EMAIL="petar.petrov@student.oulu.fi"
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