BBtools specify java temp dir (or other java options)

Question

[FGV]

Is it possible to provide other java options (e.g.) -Djava.io.tmpdir to bbtools? As far as I can see, only -Xmx works.

[GenoMax]

You could edit the wrapper script (e.g. bbmap.sh) and directly add the java option to the local CMD.

local CMD="java $EA $EOOM $z $z2 -Djava.io.tmpdir=/path_to/dir $JNI -cp $CP align2.BBMap build=1 overwrite=true fastareadlen=500 $@"

[FGV]

I was trying to avoid changing BBtools code. :)

[GenoMax]

You are not changing BBTools code. This is just a shell wrapper script around the actual code :-)

It should work. Did you try it?