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authorbrobr <sborg63@disroot.org>2022-01-31 22:41:13 +0000
committerWilly Sudiarto Raharjo <willysr@slackbuilds.org>2022-02-02 23:24:38 +0700
commit722ab55e5249c54c42ef07aa1dabd770745ce9d4 (patch)
tree75832f6480a26ed4333c0be2011258074f478d31 /academic/STAR
parent07c418576338c596ca746dd8438401c8bd000a2a (diff)
downloadslackbuilds-722ab55e5249c54c42ef07aa1dabd770745ce9d4.tar.gz
academic/STAR: Updated to version 2.7.10a
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic/STAR')
-rw-r--r--academic/STAR/README15
-rw-r--r--academic/STAR/STAR.SlackBuild25
-rw-r--r--academic/STAR/STAR.info6
3 files changed, 36 insertions, 10 deletions
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 <sborg63@disroot.org>
+# Copyright 2018-2022 Rob van Nues <sborg63@disroot.org>
# 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"