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| -rw-r--r-- | academic/jellyfish_k-mer/README | 12 | ||||
| -rw-r--r-- | academic/jellyfish_k-mer/jellyfish_k-mer.SlackBuild | 103 | ||||
| -rw-r--r-- | academic/jellyfish_k-mer/jellyfish_k-mer.info | 10 | ||||
| -rw-r--r-- | academic/jellyfish_k-mer/slack-desc | 19 |
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: |