academic/tabix-legacy: Added (Generic indexer).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

4 files changed, 148 insertions, 0 deletions

diff --git a/academic/tabix-legacy/README b/academic/tabix-legacy/README
new file mode 100644
index 0000000000000..ca2ddbbe869b9
--- /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 0000000000000..092607218c823
--- /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 0000000000000..5ca182d6113a6
--- /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 0000000000000..84be3e93ecd0e
--- /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"