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| -rw-r--r-- | academic/seqkit/README | 26 | ||||
| -rw-r--r-- | academic/seqkit/seqkit.SlackBuild | 73 | ||||
| -rw-r--r-- | academic/seqkit/seqkit.info | 10 | ||||
| -rw-r--r-- | academic/seqkit/slack-desc | 19 |
4 files changed, 128 insertions, 0 deletions
diff --git a/academic/seqkit/README b/academic/seqkit/README new file mode 100644 index 0000000000..d78d8069cd --- /dev/null +++ b/academic/seqkit/README @@ -0,0 +1,26 @@ +SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file +manipulation + +FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide +and protein sequences. Common manipulations of FASTA/Q file include +converting, searching, filtering, deduplication, splitting, shuffling, +and sampling. Existing tools only implement some of these manipulations, +and not particularly efficiently, and some are only available for +certain operating systems. Furthermore, the complicated installation +process of required packages and running environments can render these +programs less user friendly. + +This project describes a cross-platform ultrafast comprehensive toolkit +for FASTA/Q processing. SeqKit provides executable binary files for all +major operating systems, including Windows, Linux, and Mac OS X, and can +be directly used without any dependencies or pre-configurations. SeqKit +demonstrates competitive performance in execution time and memory usage +compared to similar tools. The efficiency and usability of SeqKit enable +researchers to rapidly accomplish common FASTA/Q file manipulations. + +Note: This just repackages the binaries provided from upstream. + +Please cite: +Wei Shen,Shuai Le,Yan Li ,Fuquan Hu. SeqKit: A Cross-Platform and +Ultrafast Toolkit for FASTA/Q File Manipulation. October 5, 2016 +https://doi.org/10.1371/journal.pone.0163962 diff --git a/academic/seqkit/seqkit.SlackBuild b/academic/seqkit/seqkit.SlackBuild new file mode 100644 index 0000000000..eee90bb1d1 --- /dev/null +++ b/academic/seqkit/seqkit.SlackBuild @@ -0,0 +1,73 @@ +#!/bin/sh + +# Slackware build script for seqkit + +# Copyright 2020 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. + +PRGNAM=seqkit +VERSION=${VERSION:-0.12.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + ARCH=$( uname -m ) +fi + +case "$ARCH" in + i?86) ARCH=i386 + BINARCH="386" + ;; + x86_64) + BINARCH="amd64" + ;; + *) + printf "\n\n%s\n" "$ARCH is not supported." + exit 1 + ;; +esac + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +tar xvf $CWD/${PRGNAM}_linux_${BINARCH}.tar.gz + +install -D -m755 $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 +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/seqkit/seqkit.info b/academic/seqkit/seqkit.info new file mode 100644 index 0000000000..92ef791811 --- /dev/null +++ b/academic/seqkit/seqkit.info @@ -0,0 +1,10 @@ +PRGNAM="seqkit" +VERSION="0.12.1" +HOMEPAGE="https://bioinf.shenwei.me/seqkit/" +DOWNLOAD="https://github.com/shenwei356/seqkit/releases/download/v0.12.1/seqkit_linux_386.tar.gz" +MD5SUM="d96307c33d0d96c236bc98a79e0dbb7f" +DOWNLOAD_x86_64="https://github.com/shenwei356/seqkit/releases/download/v0.12.1/seqkit_linux_amd64.tar.gz" +MD5SUM_x86_64="f12da2507d4a6debf8b09ea9cc5db3f1" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/seqkit/slack-desc b/academic/seqkit/slack-desc new file mode 100644 index 0000000000..5cbf1904cb --- /dev/null +++ b/academic/seqkit/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------------------------------------------------------| +seqkit: seqkit (Ultrafast toolkit for FASTA/Q file manipulation) +seqkit: +seqkit: A cross-platform ultrafast comprehensive toolkit for FASTA/Q +seqkit: processing. +seqkit: +seqkit: https://bioinf.shenwei.me/seqkit/ +seqkit: https://github.com/shenwei356/seqkit +seqkit: https://doi.org/10.1371/journal.pone.0163962 +seqkit: +seqkit: +seqkit: |