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freebsd
GitHub Repository: freebsd/freebsd-ports-gnome
 Path: blob/main/biology/bbmap/files/patch-calcmem.sh
17391 views
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--- calcmem.sh.orig	2021-04-13 14:05:28 UTC

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+++ calcmem.sh

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@@ -72,30 +72,6 @@ function setEnvironment(){

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 	if [[ $SHIFTER_RUNTIME == 1 ]]; then

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 		#Ignore NERSC_HOST

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 		shifter=1

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-	elif [ -v "$EC2_HOME" ]; then

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-		#Let's assume this is the AWS taxonomy server...

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-		PATH=/test1/binaries/bgzip:$PATH

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-		PATH=/test1/binaries/lbzip2/bin:$PATH

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-		PATH=/test1/binaries/sambamba:$PATH

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-		#PATH=/test1/binaries/java/jdk-11.0.2/bin:$PATH

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-		PATH=/test1/binaries/pigz2/pigz-2.4:$PATH

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-	elif [ -z "$NERSC_HOST" ]; then

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-		#Not NERSC; do nothing

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-		:

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-	else

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-		PATH=/global/projectb/sandbox/gaag/bbtools/bgzip:$PATH

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-		PATH=/global/projectb/sandbox/gaag/bbtools/lbzip2/bin:$PATH

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-		PATH=/global/projectb/sandbox/gaag/bbtools/sambamba:$PATH

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-		PATH=/global/projectb/sandbox/gaag/bbtools/java/jdk-11.0.2/bin:$PATH

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-		PATH=/global/projectb/sandbox/gaag/bbtools/pigz2/pigz-2.4:$PATH

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-		

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-		if [[ $NERSC_HOST == cori ]]; then

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-

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-			#module unload PrgEnv-intel

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-			#module load PrgEnv-gnu/7.1

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-			PATH=/global/projectb/sandbox/gaag/bbtools/samtools_cori/bin:$PATH

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-			:

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-		fi

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 	fi

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 }

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