Increase BEAS2 stack size

[richelbilderbeek]

From Jeff Chang:

Hi Richel,

Thank you very much for creating the babette package. I am really enjoying using it to generate phylogenies from BEAST2.

I am generating some rather large trees (> 5000 tips) using single cell data and running into java.lang.StackOverflowError exceptions. I have been able to work around this by modifying the calls to BeastLauncher in two places in the beastier package:

perl -i -p -e 's/"-cp"/"-Xss2m", "-cp"/' \
  /usr/local/src/beastier-master/R/create_beast2_validate_cmd.R
perl -i -p -e 's/"-cp"/"-Xss2m", "-cp"/' \
  /usr/local/src/beastier-master/R/create_beast2_continue_cmd_from_options.R

This increases the stack space using the "-Xss2m" flag.

Probably a better solution would be to let the user specify the desired stack size. However, hardcoding the stack size works good enough for my use. I wanted to be aware of this limit, in case others were also using it for large trees.

Thanks,
Jeff

[richelbilderbeek]

This is awesome!

Also, I think this should be easily do-able, by adding it to the beast2_options. I will do so, if Jeff volunteers to test.