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 <willysr@slackbuilds.org>
---
 academic/STAR/README          | 15 +++++++++++++--
 academic/STAR/STAR.SlackBuild | 25 ++++++++++++++++++++-----
 academic/STAR/STAR.info       |  6 +++---
 3 files changed, 36 insertions(+), 10 deletions(-)

(limited to 'academic')

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"
-- 
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