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>

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: