Dropulation java heap size -m option error

[drneavin]

Tool(s) involved

AssignCellsToSamples and DetectDoublets

Description

The help message for AssignCellsToSamples and DetectDoublets indicates that the java heap size can be indicated with the -m parameter:

USAGE: /directflow/SCCGGroupShare/projects/DrewNeavin/software/Drop-seq_tools-2.5.1/AssignCellsToSamples [-m <jvm_heap_size>] [-v] program args...
       -m <jvm_heap_size> (default 4g)
       -v echo final command line before executing

but when I try to set this I get the following error:

-m is not a recognized option

Would be good to update the help text or update so that this option can be used.

Thanks!

[jamesnemesh]

Just to check:

When you're invoking tools, are you using invoking the tool with the memory option first?

AssignCellsToSamples -m 8g [standard options]

If you look at the deployed tool AssignCellsToSamples, it's a shell script that defers to the jar file and passes in your -m option to the typical java heap syntax and then passes on all the other arguments.

while getopts ":m:vh" options; do
  case $options in
    m ) xmx=$OPTARG;;

[...]

java -Xmx${xmx} -XX:+UseParallelOldGC -XX:ParallelGCThreads=1 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+HeapDumpOnOutOfMemoryError -Djava.io.tmpdir=$TMPDIR -jar $jar_deploy_dir/dropseq.jar $progname $*

This should be the same as this command, which you could use if you preferred more direct control of other java options.

java -Xmx8g -jar dropseq.jar AssignCellsToSamples

[drneavin]

Thanks @jamesnemesh, I think I was invoking it as the first parameter but may not have been. Good to know the alternative execution method that can be used as well to indicate different java parameters.