From b58f460047df0774b19d1308131523aaa520cfa2 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Fri, 27 Mar 2015 07:54:43 +0700 Subject: academic/cutadapt: Added (Trim adapters). Signed-off-by: Willy Sudiarto Raharjo --- academic/cutadapt/README | 26 +++++++++++ academic/cutadapt/cutadapt.SlackBuild | 85 +++++++++++++++++++++++++++++++++++ academic/cutadapt/cutadapt.info | 10 +++++ academic/cutadapt/slack-desc | 19 ++++++++ 4 files changed, 140 insertions(+) create mode 100644 academic/cutadapt/README create mode 100644 academic/cutadapt/cutadapt.SlackBuild create mode 100644 academic/cutadapt/cutadapt.info create mode 100644 academic/cutadapt/slack-desc (limited to 'academic/cutadapt') diff --git a/academic/cutadapt/README b/academic/cutadapt/README new file mode 100644 index 0000000000..a558d53867 --- /dev/null +++ b/academic/cutadapt/README @@ -0,0 +1,26 @@ +Cutadapt: trim adapters from high-throughput sequencing reads + +Cutadapt finds and removes adapter sequences, primers, poly-A tails +and other types of unwanted sequence from your high-throughput +sequencing reads. + +Cleaning your data in this way is often required: Reads from small-RNA +sequencing contain the 3’ sequencing adapter because the read is +longer than the molecule that is sequenced. Amplicon reads start with +a primer sequence. Poly-A tails are useful for pulling out RNA from +your sample, but often you don’t want them to be in your reads. + +Cutadapt helps with these trimming tasks by finding the adapter or +primer sequences in an error-tolerant way. It can also modify and +filter reads in various ways. Adapter sequences can contain IUPAC +wildcard characters. Also, paired-end reads and even colorspace data +is supported. If you want, you can also just demultiplex your input +data, without removing adapter sequences at all. + +Cutadapt comes with an extensive suite of automated tests and is +available under the terms of the MIT license. + +If you use cutadapt, please cite: +Marcel Martin. Cutadapt removes adapter sequences from high-throughput +sequencing reads. EMBnet.journal, 17(1):10-12, May 2011. DOI: +http://dx.doi.org/10.14806/ej.17.1.200 diff --git a/academic/cutadapt/cutadapt.SlackBuild b/academic/cutadapt/cutadapt.SlackBuild new file mode 100644 index 0000000000..8837ae02c4 --- /dev/null +++ b/academic/cutadapt/cutadapt.SlackBuild @@ -0,0 +1,85 @@ +#!/bin/sh + +# Slackware build script for cutadapt + +# Copyright 2015 Petar Petrov petar.petrov@student.oulu.fi +# 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=cutadapt +VERSION=${VERSION:-1.8} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -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 +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 {} \; + +python setup.py install --root=$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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a CHANGES.rst CITATION LICENSE README.rst $PKG/usr/doc/$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/cutadapt/cutadapt.info b/academic/cutadapt/cutadapt.info new file mode 100644 index 0000000000..115c60b2f5 --- /dev/null +++ b/academic/cutadapt/cutadapt.info @@ -0,0 +1,10 @@ +PRGNAM="cutadapt" +VERSION="1.8" +HOMEPAGE="https://pypi.python.org/pypi/cutadapt/" +DOWNLOAD="https://pypi.python.org/packages/source/c/cutadapt/cutadapt-1.8.tar.gz" +MD5SUM="73cc9c52d1b14883c24a4c29b16e0b61" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="petar.petrov@student.oulu.fi" diff --git a/academic/cutadapt/slack-desc b/academic/cutadapt/slack-desc new file mode 100644 index 0000000000..b4a0da5f16 --- /dev/null +++ b/academic/cutadapt/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------------------------------------------------------| +cutadapt: cutadapt (Trim adapters from high-throughput sequencing reads) +cutadapt: +cutadapt: Cutadapt finds and removes adapter sequences, primers, poly-A +cutadapt: tails and other types of unwanted sequence from your high- +cutadapt: throughput sequencing reads. +cutadapt: +cutadapt: Home: https://pypi.python.org/pypi/cutadapt/ +cutadapt: Reference: /usr/doc/cutadapt-1.8/CITATION +cutadapt: +cutadapt: +cutadapt: -- cgit v1.2.3