From 87f60da8dead64a7e438ea4e1186807adb7c7212 Mon Sep 17 00:00:00 2001 From: Rob van Nues Date: Sun, 10 Sep 2017 12:44:14 +0100 Subject: academic/flexbar: Added (barcode and adapter removal). Signed-off-by: David Spencer --- academic/flexbar/README | 18 +++++++ academic/flexbar/flexbar.SlackBuild | 101 ++++++++++++++++++++++++++++++++++++ academic/flexbar/flexbar.info | 12 +++++ academic/flexbar/slack-desc | 19 +++++++ 4 files changed, 150 insertions(+) create mode 100644 academic/flexbar/README create mode 100644 academic/flexbar/flexbar.SlackBuild create mode 100644 academic/flexbar/flexbar.info create mode 100644 academic/flexbar/slack-desc diff --git a/academic/flexbar/README b/academic/flexbar/README new file mode 100644 index 0000000000..ed016820d8 --- /dev/null +++ b/academic/flexbar/README @@ -0,0 +1,18 @@ +The program Flexbar preprocesses high-throughput sequencing data +efficiently. It demultiplexes barcoded runs and removes adapter +sequences. Moreover, trimming and filtering features are provided. +Flexbar increases read mapping rates and improves genome as well as +transcriptome assemblies. It supports next-generation sequencing data +in fasta and fastq format, e.g. from Roche 454 and the Illumina +platform. + +The script downloads the segan-library needed for compilation. + +References + +Johannes T. Roehr, Christoph Dieterich, Knut Reinert: +Flexbar 3.0 - SIMD and multicore parallelization. Bioinformatics 2017. + +Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: +Flexbar - flexible barcode and adapter processing for next-generation +sequencing platforms. Biology 2012. diff --git a/academic/flexbar/flexbar.SlackBuild b/academic/flexbar/flexbar.SlackBuild new file mode 100644 index 0000000000..4155605bae --- /dev/null +++ b/academic/flexbar/flexbar.SlackBuild @@ -0,0 +1,101 @@ +#!/bin/sh + +# Slackware build script for flexbar + +# Copyright 2017 Rob van Nues +# 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=flexbar +VERSION=${VERSION:-3.0.3} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +LIBNAM=seqan-library +LIBVER=${LIBVER:-2.2.0} + +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 $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +tar xvf $CWD/$LIBNAM-$LIBVER.tar.xz $LIBNAM-$LIBVER/include/ --strip-components=1 +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 {} \; + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + make +cd .. + +install -D -m755 build/$PRGNAM $PKG/usr/bin/$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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + README.md LICENSE.md \ + $PKG/usr/doc/$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/flexbar/flexbar.info b/academic/flexbar/flexbar.info new file mode 100644 index 0000000000..c84d4df37d --- /dev/null +++ b/academic/flexbar/flexbar.info @@ -0,0 +1,12 @@ +PRGNAM="flexbar" +VERSION="3.0.3" +HOMEPAGE="https://github.com/seqan/flexbar" +DOWNLOAD="https://github.com/seqan/flexbar/archive/v3.0.3/flexbar-3.0.3.tar.gz \ + https://github.com/seqan/seqan/releases/download/seqan-v2.2.0/seqan-library-2.2.0.tar.xz" +MD5SUM="16bbdc3eb89a82f9879655e33c147451 \ + 0070e035ac84c3c128b0e8dd2737b2d3" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="tbb" +MAINTAINER="Rob van Nues" +EMAIL="rvnues at tesco {dot} net" diff --git a/academic/flexbar/slack-desc b/academic/flexbar/slack-desc new file mode 100644 index 0000000000..4c2c9b2ef8 --- /dev/null +++ b/academic/flexbar/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------------------------------------------------------| +flexbar: flexbar (barcode and adapter removal) +flexbar: +flexbar: The program Flexbar preprocesses high-throughput sequencing data +flexbar: efficiently. It demultiplexes barcoded runs and removes adapter +flexbar: sequences. Moreover, trimming and filtering features are provided. +flexbar: Flexbar increases read mapping rates and improves genome as well as +flexbar: transcriptome assemblies. It supports next-generation sequencing data +flexbar: in fasta and fastq format, e.g. from Roche 454 and the Illumina +flexbar: platform. +flexbar: +flexbar: https://github.com/seqan/flexbar -- cgit v1.2.3