From 201f40382197fbf0baf90fbafd016efb5567a7f8 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Mon, 24 Dec 2018 10:56:58 +0700 Subject: academic/tabix-legacy: Added (Generic indexer). Signed-off-by: Willy Sudiarto Raharjo --- academic/tabix-legacy/README | 14 ++++ academic/tabix-legacy/slack-desc | 19 +++++ academic/tabix-legacy/tabix-legacy.SlackBuild | 105 ++++++++++++++++++++++++++ academic/tabix-legacy/tabix-legacy.info | 10 +++ 4 files changed, 148 insertions(+) create mode 100644 academic/tabix-legacy/README create mode 100644 academic/tabix-legacy/slack-desc create mode 100644 academic/tabix-legacy/tabix-legacy.SlackBuild create mode 100644 academic/tabix-legacy/tabix-legacy.info (limited to 'academic/tabix-legacy') diff --git a/academic/tabix-legacy/README b/academic/tabix-legacy/README new file mode 100644 index 0000000000..ca2ddbbe86 --- /dev/null +++ b/academic/tabix-legacy/README @@ -0,0 +1,14 @@ +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. + +NOTE! +Tabix is now included in htslib. This is an older version of the +program, kept here for compatibility with Ugene. You can safely install +it along htslib. When you start Ugene, go to Settings > Preferences > +External Tools and manually select the legacy binary in /usr/bin/ diff --git a/academic/tabix-legacy/slack-desc b/academic/tabix-legacy/slack-desc new file mode 100644 index 0000000000..092607218c --- /dev/null +++ b/academic/tabix-legacy/slack-desc @@ -0,0 +1,19 @@ +# 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-legacy: tabix-legacy (Legacy version of Tabix) +tabix-legacy: +tabix-legacy: Tabix indexes a TAB-delimited genome position file in.tab.bgz +tabix-legacy: and creates an index file in.tab.bgz.tbi when region is absent +tabix-legacy: from the command-line. The input data file must be position +tabix-legacy: sorted and compressed by bgzip which has a gzip like interface. +tabix-legacy: Tabix is able to quickly retrieve data lines overlapping regions +tabix-legacy: specified in the format "chr:beginPos-endPos". +tabix-legacy: +tabix-legacy: Home: http://samtools.sourceforge.net/tabix.shtml +tabix-legacy: diff --git a/academic/tabix-legacy/tabix-legacy.SlackBuild b/academic/tabix-legacy/tabix-legacy.SlackBuild new file mode 100644 index 0000000000..5ca182d611 --- /dev/null +++ b/academic/tabix-legacy/tabix-legacy.SlackBuild @@ -0,0 +1,105 @@ +#!/bin/sh + +# Slackware build script for tabix-legacy + +# Copyright 2013-2018 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. + +SRCNAM=tabix +SUFFIX=legacy +PRGNAM=${SRCNAM}-${SUFFIX} +VERSION=${VERSION:-0.2.6} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -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 $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.bz2 +cd $SRCNAM-$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 $PKG/usr/bin/tabix-$SUFFIX +install -D -m755 bgzip $PKG/usr/bin/bgzip-$SUFFIX + +# Place manpage +install -D -m644 $SRCNAM.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-legacy/tabix-legacy.info b/academic/tabix-legacy/tabix-legacy.info new file mode 100644 index 0000000000..84be3e93ec --- /dev/null +++ b/academic/tabix-legacy/tabix-legacy.info @@ -0,0 +1,10 @@ +PRGNAM="tabix-legacy" +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