From 722ab55e5249c54c42ef07aa1dabd770745ce9d4 Mon Sep 17 00:00:00 2001 From: brobr Date: Mon, 31 Jan 2022 22:41:13 +0000 Subject: academic/STAR: Updated to version 2.7.10a Signed-off-by: Willy Sudiarto Raharjo --- academic/STAR/README | 15 +++++++++++++-- academic/STAR/STAR.SlackBuild | 25 ++++++++++++++++++++----- academic/STAR/STAR.info | 6 +++--- 3 files changed, 36 insertions(+), 10 deletions(-) (limited to 'academic/STAR') diff --git a/academic/STAR/README b/academic/STAR/README index 7d410d628f..ae22618ac8 100644 --- a/academic/STAR/README +++ b/academic/STAR/README @@ -2,9 +2,20 @@ STAR aligns short and long RNA-seq reads to a reference genome using uncompressed suffix arrays, resulting in fast, accurate mapping. STAR is capable of unbiased de novo detection of canonical splice junctions, can discover non-canonical splices and chimeric (fusion) -transcripts and can map full-length RNA sequences. Comes with -STARsolo for: mapping, demultiplexing and gene quantification for +transcripts and can map full-length RNA sequences. Comes with +STARsolo for: mapping, demultiplexing and gene quantification for single cell RNA-seq (See STARmanual). +The make command for building the program assumes that the cpu is +supporting AVX extensions, included in intel processors since Sandy +Bridge (2008) and in AMD cpus since Bulldozer (2011). See the +Slackbuild if other processors can be supported. Reference: https://www.ncbi.nlm.nih.gov/pubmed/23104886 + + +LIMITATIONS +This release was tested with the default parameters for human and +mouse genomes. Mammal genomes require at least 16GB of RAM, ideally +32GB. Please contact the author for a list of recommended parameters +for much larger or much smaller genomes. diff --git a/academic/STAR/STAR.SlackBuild b/academic/STAR/STAR.SlackBuild index f5abdc97dd..c72e15ed31 100644 --- a/academic/STAR/STAR.SlackBuild +++ b/academic/STAR/STAR.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for STAR -# Copyright 2018-2021 Rob van Nues +# Copyright 2018-2022 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,10 +25,18 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=STAR -VERSION=${VERSION:-2.7.9a} +VERSION=${VERSION:-2.7.10a} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} +# This script is set for processors that support "Advanced Vector Extensions", +# (AVX), included since 2008 in Intel processors (Sandy Bridge) and since 2011 +# in AMD cpus (Bulldozer). AVX is an implementation of "Single Instruction +# stream-Multiple Data streams" (SIMD) to process vector type data. +# If no AVX (`cat /proc/cpuinfo | grep 'avx'`) is present, specify the +# available SIMD architecture (https://en.wikichip.org/wiki/x86/extensions), +# e.g. with "Streaming SIMD Extensions" use 'sse', and uncomment the next line. +#SIMD=${SIMD:-sse}; echo "Using ${SIMD} as SIMD" if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -55,7 +63,7 @@ if [ "$ARCH" = "x86_64" ]; then LIBDIRSUFFIX="64" else echo "Sorry, this program does not run/compile on your architecture ($ARCH)" - exit 1 + exit 0 fi set -e @@ -83,9 +91,16 @@ find -L . \ # https://github.com/alexdobin/STAR/issues/447 #so let's forget about this for now +#For processors that do not support AVX extensions, specify the target SIMD architecture +#make STAR CXXFLAGS_SIMD=sse cd source - - make ${PRGNAM} CFLAGS="$SLKCFLAGS" CXXFLAGSextra="$SLKCFLAGS" + if [ ! -z "${SIMD}" ]; then + echo "make with CXXFLAG_SIMD=${SIMD}" + make ${PRGNAM} CFLAGS="$SLKCFLAGS" CXXFLAGSextra="$SLKCFLAGS" CXXFLAGS_SIMD="$SIMD" + else + echo "default make" + make ${PRGNAM} CFLAGS="$SLKCFLAGS" CXXFLAGSextra="$SLKCFLAGS" + fi mkdir -p $PKG/usr/bin install -Dm755 $PRGNAM "$PKG/usr/bin/${PRGNAM}" diff --git a/academic/STAR/STAR.info b/academic/STAR/STAR.info index 4c3a22024f..939f358cb0 100644 --- a/academic/STAR/STAR.info +++ b/academic/STAR/STAR.info @@ -1,10 +1,10 @@ PRGNAM="STAR" -VERSION="2.7.9a" +VERSION="2.7.10a" HOMEPAGE="https://github.com/alexdobin/STAR" DOWNLOAD="UNSUPPORTED" MD5SUM="" -DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.7.9a/STAR-2.7.9a.tar.gz" -MD5SUM_x86_64="432c55d7ee7223c9099206a697bd9c30" +DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.7.10a/STAR-2.7.10a.tar.gz" +MD5SUM_x86_64="8f0c982f946e1b93a0f499ab44a4b040" REQUIRES="" MAINTAINER="Rob van Nues" EMAIL="sborg63@disroot.org" -- cgit v1.2.3