From 3b0f2073eec677f37bf01c825e9b8652a209f5be Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sun, 12 Jan 2020 12:10:47 +0100 Subject: academic/tabix: Removed. Signed-off-by: Matteo Bernardini --- academic/tabix/README | 8 ---- academic/tabix/slack-desc | 19 -------- academic/tabix/tabix.SlackBuild | 103 ---------------------------------------- academic/tabix/tabix.info | 10 ---- 4 files changed, 140 deletions(-) delete mode 100644 academic/tabix/README delete mode 100644 academic/tabix/slack-desc delete mode 100644 academic/tabix/tabix.SlackBuild delete mode 100644 academic/tabix/tabix.info diff --git a/academic/tabix/README b/academic/tabix/README deleted file mode 100644 index 143a5d5684..0000000000 --- a/academic/tabix/README +++ /dev/null @@ -1,8 +0,0 @@ -Tabix indexes a TAB-delimited genome position file in.tab.bgz and -creates an index file in.tab.bgz.tbi when region is absent from the -command-line. The input data file must be position sorted and -compressed by bgzip which has a gzip like interface. After indexing, -tabix is able to quickly retrieve data lines overlapping regions -specified in the format "chr:beginPos-endPos". Fast data retrieval -also works over network if URI is given as a file name and in this -case the index file will be downloaded if it is not present locally. diff --git a/academic/tabix/slack-desc b/academic/tabix/slack-desc deleted file mode 100644 index 5a387152f0..0000000000 --- a/academic/tabix/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# HOW TO EDIT THIS FILE: -# The "handy ruler" below makes it easier to edit a package description. -# Line up the first '|' above the ':' following the base package name, and -# the '|' on the right side marks the last column you can put a character in. -# You must make exactly 11 lines for the formatting to be correct. It's also -# customary to leave one space after the ':' except on otherwise blank lines. - - |-----handy-ruler------------------------------------------------------| -tabix: tabix (Generic indexer for TAB-delimited genome position files) -tabix: -tabix: Tabix indexes a TAB-delimited genome position file in.tab.bgz -tabix: and creates an index file in.tab.bgz.tbi when region is absent -tabix: from the command-line. The input data file must be position -tabix: sorted and compressed by bgzip which has a gzip like interface. -tabix: Tabix is able to quickly retrieve data lines overlapping regions -tabix: specified in the format "chr:beginPos-endPos". -tabix: -tabix: Home: http://samtools.sourceforge.net/tabix.shtml -tabix: diff --git a/academic/tabix/tabix.SlackBuild b/academic/tabix/tabix.SlackBuild deleted file mode 100644 index 017733aaa0..0000000000 --- a/academic/tabix/tabix.SlackBuild +++ /dev/null @@ -1,103 +0,0 @@ -#!/bin/sh - -# Slackware build script for tabix - -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com -# All rights reserved. -# -# Redistribution and use of this script, with or without modification, is -# permitted provided that the following conditions are met: -# -# 1. Redistributions of this script must retain the above copyright -# notice, this list of conditions and the following disclaimer. -# -# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED -# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO -# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, -# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR -# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF -# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -PRGNAM=tabix -VERSION=${VERSION:-0.2.6} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i486 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - -CWD=$(pwd) -TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM -OUTPUT=${OUTPUT:-/tmp} - -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - -set -e - -rm -rf $PKG -mkdir -p $TMP $PKG $OUTPUT -cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2 -cd $PRGNAM-$VERSION -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 {} \; - -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -make - -# Install executables -install -D -m755 tabix $PKG/usr/bin/tabix -install -D -m755 bgzip $PKG/usr/bin/bgzip - -# Place manpage -install -D -m644 $PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1 - -# Include examples -mkdir -p $PKG/usr/share/$PRGNAM -cp -a example.gtf.gz example.gtf.gz.tbi $PKG/usr/share/$PRGNAM - -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 $PKG/usr/doc/$PRGNAM-$VERSION -cp -a \ - ChangeLog NEWS \ - $PKG/usr/doc/$PRGNAM-$VERSION -cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild - -mkdir -p $PKG/install -cat $CWD/slack-desc > $PKG/install/slack-desc - -cd $PKG -/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/tabix/tabix.info b/academic/tabix/tabix.info deleted file mode 100644 index bac2016304..0000000000 --- a/academic/tabix/tabix.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="tabix" -VERSION="0.2.6" -HOMEPAGE="http://samtools.sourceforge.net/tabix.shtml" -DOWNLOAD="http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2" -MD5SUM="36a61ceac2f5bed36018434282bbcc5d" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="" -MAINTAINER="Petar Petrov" -EMAIL="slackalaxy@gmail.com" -- cgit v1.2.3