Commit b1a11c26 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 38.43+dfsg

parent 41c2d0b5

README.md

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@@ -3,4 +3,4 @@ 
# Language: Java, Bash

# Information about documentation is in /docs/readme.txt.



# Version 38.26
 
# Version 38.43

a_sample_mt.sh

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None yet!



Java Parameters:

-Xmx            This will be passed to Java to set memory usage, overriding the program's automatic memory detection.

                -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.  The max is typically 85% of physical memory.

-eoom           This flag will cause the process to exit if an out-of-memory exception occurs.  Requires Java 8u92+.

-Xmx            This will set Java's memory usage, overriding autodetection.

                -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will

                specify 200 megs. The max is typically 85% of physical memory.

-eoom           This flag will cause the process to exit if an out-of-memory

                exception occurs.  Requires Java 8u92+.

-da             Disable assertions.



Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.

analyzeaccession.sh

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lines=-1        If positive, stop after this many lines.



Java Parameters:

-Xmx            This will be passed to Java to set memory usage, overriding the program's automatic memory detection.

                -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.  The max is typically 85% of physical memory.

-eoom           This flag will cause the process to exit if an out-of-memory exception occurs.  Requires Java 8u92+.

-Xmx            This will set Java's memory usage, overriding autodetection.

                -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will

                specify 200 megs. The max is typically 85% of physical memory.

-eoom           This flag will cause the process to exit if an out-of-memory

                exception occurs.  Requires Java 8u92+.

-da             Disable assertions.



Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.

analyzegenes.sh

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@@ -74,7 +74,7 @@ function analyze() { 
		module load pigz

	fi

	local CMD="java $EA $EOOM $z $z2 -cp $CP prok.AnalyzeGenes $@"

	echo $CMD >&2

	#echo $CMD >&2

	eval $CMD

}

bbcms.sh

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usage(){

echo "

Written by Brian Bushnell

Last modified July 24, 2018

Last modified December 19, 2018



Description:  Error corrects reads and/or filters by depth, storing

kmer counts in a count-min sketch (a Bloom filter variant).
@@ -89,9 +89,11 @@ smooth=3 Remove spikes from kmer counts due to hash collisions. 
                



Java Parameters:

-Xmx            This will be passed to Java to set memory usage, overriding the program's automatic memory detection.

                -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.  The max is typically 85% of physical memory.

-eoom           This flag will cause the process to exit if an out-of-memory exception occurs.  Requires Java 8u92+.

-Xmx            This will set Java's memory usage, overriding autodetection.

                -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will

                specify 200 megs. The max is typically 85% of physical memory.

-eoom           This flag will cause the process to exit if an out-of-memory

                exception occurs.  Requires Java 8u92+.

-da             Disable assertions.



Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.