From a024c5f014cad2e7e5e7f4789d4d2862799bab73 Mon Sep 17 00:00:00 2001 From: William PC Date: Thu, 16 Mar 2023 18:55:49 +0000 Subject: [PATCH] academic/pomoxis: Added (bioinformatics tools for nanopore research) Signed-off-by: bedlam Signed-off-by: Willy Sudiarto Raharjo --- academic/pomoxis/README | 4 ++ academic/pomoxis/pomoxis.SlackBuild | 102 ++++++++++++++++++++++++++++ academic/pomoxis/pomoxis.info | 10 +++ academic/pomoxis/slack-desc | 19 ++++++ 4 files changed, 135 insertions(+) create mode 100644 academic/pomoxis/README create mode 100644 academic/pomoxis/pomoxis.SlackBuild create mode 100644 academic/pomoxis/pomoxis.info create mode 100644 academic/pomoxis/slack-desc diff --git a/academic/pomoxis/README b/academic/pomoxis/README new file mode 100644 index 0000000000..5214c86dc4 --- /dev/null +++ b/academic/pomoxis/README @@ -0,0 +1,4 @@ + Pomoxis comprises a set of basic bioinformatic tools tailored to +nanopore sequencing. Notably tools are included for generating and +analysing draft assemblies. Many of these tools are used by the +research data analysis group at Oxford Nanopore Technologies. diff --git a/academic/pomoxis/pomoxis.SlackBuild b/academic/pomoxis/pomoxis.SlackBuild new file mode 100644 index 0000000000..6c43667b34 --- /dev/null +++ b/academic/pomoxis/pomoxis.SlackBuild @@ -0,0 +1,102 @@ +#!/bin/bash + +# Slackware build script for pomoxis + +# Copyright 2023 William PC - Seattle, USA +# 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. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=pomoxis +VERSION=${VERSION:-0.3.12} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +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 +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 {} \; + + +python3 setup.py install --root=$PKG + + +# Don't ship .la files: +rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la + +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 \ + CHANGELOG.md LICENSE.md docs \ + $PKG/usr/doc/$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 diff --git a/academic/pomoxis/pomoxis.info b/academic/pomoxis/pomoxis.info new file mode 100644 index 0000000000..e78d77e751 --- /dev/null +++ b/academic/pomoxis/pomoxis.info @@ -0,0 +1,10 @@ +PRGNAM="pomoxis" +VERSION="0.3.12" +HOMEPAGE="https://github.com/nanoporetech/pomoxis" +DOWNLOAD="https://github.com/nanoporetech/pomoxis/archive/v0.3.12/pomoxis-0.3.12.tar.gz" +MD5SUM="a2c01f36a87982962143f8d99648a7f1" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="blas" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/academic/pomoxis/slack-desc b/academic/pomoxis/slack-desc new file mode 100644 index 0000000000..8d2494de50 --- /dev/null +++ b/academic/pomoxis/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------------------------------------------------------| +pomoxis: pomoxis (bioinformatics tools for nanopore research) +pomoxis: +pomoxis: +pomoxis: Pomoxis comprises a set of basic bioinformatic tools tailored to +pomoxis: nanopore sequencing. Notably tools are included for generating and +pomoxis: analysing draft assemblies. Many of these tools are used by the +pomoxis: research data analysis group at Oxford Nanopore Technologies. +pomoxis: +pomoxis: +pomoxis: +pomoxis: