academic/seqkit: Added (toolkit for FASTA/Q file manipulation)
Signed-off-by: Dave Woodfall <dave@slackbuilds.org> Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
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SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file
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manipulation
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FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide
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and protein sequences. Common manipulations of FASTA/Q file include
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converting, searching, filtering, deduplication, splitting, shuffling,
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and sampling. Existing tools only implement some of these manipulations,
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and not particularly efficiently, and some are only available for
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certain operating systems. Furthermore, the complicated installation
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process of required packages and running environments can render these
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programs less user friendly.
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This project describes a cross-platform ultrafast comprehensive toolkit
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for FASTA/Q processing. SeqKit provides executable binary files for all
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major operating systems, including Windows, Linux, and Mac OS X, and can
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be directly used without any dependencies or pre-configurations. SeqKit
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demonstrates competitive performance in execution time and memory usage
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compared to similar tools. The efficiency and usability of SeqKit enable
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researchers to rapidly accomplish common FASTA/Q file manipulations.
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Note: This just repackages the binaries provided from upstream.
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Please cite:
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Wei Shen,Shuai Le,Yan Li ,Fuquan Hu. SeqKit: A Cross-Platform and
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Ultrafast Toolkit for FASTA/Q File Manipulation. October 5, 2016
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https://doi.org/10.1371/journal.pone.0163962
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#!/bin/sh
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# Slackware build script for seqkit
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# Copyright 2020 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=seqkit
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VERSION=${VERSION:-0.12.1}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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ARCH=$( uname -m )
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fi
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case "$ARCH" in
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i?86) ARCH=i386
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BINARCH="386"
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;;
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x86_64)
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BINARCH="amd64"
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;;
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*)
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printf "\n\n%s\n" "$ARCH is not supported."
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exit 1
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;;
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esac
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM-$VERSION
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mkdir $PRGNAM-$VERSION
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tar xvf $CWD/${PRGNAM}_linux_${BINARCH}.tar.gz
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install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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PRGNAM="seqkit"
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VERSION="0.12.1"
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HOMEPAGE="https://bioinf.shenwei.me/seqkit/"
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DOWNLOAD="https://github.com/shenwei356/seqkit/releases/download/v0.12.1/seqkit_linux_386.tar.gz"
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MD5SUM="d96307c33d0d96c236bc98a79e0dbb7f"
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DOWNLOAD_x86_64="https://github.com/shenwei356/seqkit/releases/download/v0.12.1/seqkit_linux_amd64.tar.gz"
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MD5SUM_x86_64="f12da2507d4a6debf8b09ea9cc5db3f1"
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REQUIRES=""
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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@ -0,0 +1,19 @@
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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seqkit: seqkit (Ultrafast toolkit for FASTA/Q file manipulation)
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seqkit:
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seqkit: A cross-platform ultrafast comprehensive toolkit for FASTA/Q
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seqkit: processing.
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seqkit:
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seqkit: https://bioinf.shenwei.me/seqkit/
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seqkit: https://github.com/shenwei356/seqkit
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seqkit: https://doi.org/10.1371/journal.pone.0163962
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seqkit:
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seqkit:
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seqkit:
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