academic/jellyfish_k-mer: Added (k-mers counting tools).

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

4 files changed, 144 insertions, 0 deletions

diff --git a/academic/jellyfish_k-mer/README b/academic/jellyfish_k-mer/README
new file mode 100644
index 0000000000..7988cded9c
--- /dev/null
+++ b/academic/jellyfish_k-mer/README
@@ -0,0 +1,12 @@
+Jellyfish is a tool for fast, memory-efficient counting of k-mers in
+DNA. A k-mer is a substring of length k, and counting the occurrences of
+all such substrings is a central step in many analyses of DNA sequence.
+Jellyfish can count k-mers quickly by using an efficient encoding of a
+hash table and by exploiting the "compare-and-swap" CPU instruction to
+increase parallelism.
+
+Jellyfish is a command-line program that reads FASTA and multi-FASTA
+files containing DNA sequences. It outputs its k-mer counts in an binary
+format, which can be translated into a human-readable text format using
+the "jellyfish dump" command. See the documentation below for more
+details.
diff --git a/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild b/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild
new file mode 100644
index 0000000000..4e22588b36
--- /dev/null
+++ b/academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild
@@ -0,0 +1,103 @@
+#!/bin/sh
+
+# Slackware build script for jellyfish
+
+# Copyright 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=jellyfish
+PRGNAM=${SRCNAM}_k-mer
+VERSION=${VERSION:-1.1.12}
+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.gz
+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" \
+./configure \
+  --prefix=/usr \
+  --libdir=/usr/lib${LIBDIRSUFFIX} \
+  --sysconfdir=/etc \
+  --localstatedir=/var \
+  --mandir=/usr/man \
+  --docdir=/usr/doc/$PRGNAM-$VERSION \
+  --build=$ARCH-slackware-linux
+
+make
+make install DESTDIR=$PKG
+
+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-$VERSION
+cp -a \
+  doc/$SRCNAM.pdf LICENSE HalfLICENSE README \
+  $PKG/usr/doc/$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/jellyfish_k-mer/jellyfish_k-mer.info b/academic/jellyfish_k-mer/jellyfish_k-mer.info
new file mode 100644
index 0000000000..6185cffa6d
--- /dev/null
+++ b/academic/jellyfish_k-mer/jellyfish_k-mer.info
@@ -0,0 +1,10 @@
+PRGNAM="jellyfish_k-mer"
+VERSION="1.1.12"
+HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
+DOWNLOAD="https://github.com/gmarcais/Jellyfish/releases/download/v1.1.12/jellyfish-1.1.12.tar.gz"
+MD5SUM="175e6fc48ca0b4ba845614cdb4467387"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"
diff --git a/academic/jellyfish_k-mer/slack-desc b/academic/jellyfish_k-mer/slack-desc
new file mode 100644
index 0000000000..c5be86dd58
--- /dev/null
+++ b/academic/jellyfish_k-mer/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------------------------------------------------------|
+jellyfish_k-mer: jellyfish_k-mer (A tool for counting of k-mers in DNA)
+jellyfish_k-mer:
+jellyfish_k-mer: Jellyfish is a tool for fast, memory-efficient counting of k-mers
+jellyfish_k-mer: in DNA. A k-mer is a substring of length k, and counting the
+jellyfish_k-mer: occurrences of all such substrings is a central step in many
+jellyfish_k-mer: analyses of DNA sequence. Jellyfish can count k-mers quickly by
+jellyfish_k-mer: using an efficient encoding of a hash table and by exploiting the
+jellyfish_k-mer: "compare-and-swap" CPU instruction to increase parallelism.
+jellyfish_k-mer:
+jellyfish_k-mer: Home: http://www.genome.umd.edu/jellyfish.html
+jellyfish_k-mer: