Wonder if anyone has any creative solutions for this one: https://github.com/nf-core/modules/blob/master/modules/nf-core/busco/busco/main.nf The BUSCO process calls

stats.sh

from the

bbtools

package. Because you can't modify the arguments to it, this has a hard-coded memory limit of 120Mb, which sometimes gives OOM errors for large genome assemblies. The BUSCO folks don't seem to be very responsive, and there's no way to set the

bbtools

java process to receive a memory setting via e.g.

JAVA_OPTS

. However, BUSCO does have a config file (TOML format) and it's possible to override the path to the

stats.sh

script. So we could write a wrapper that calls

stats.sh

with an increased amount of memory, and set this as the call in a config file. But the config file is also an optional input into the process, so we would somehow have to append this to the config if supplied. Is this a ridiculous idea, should we just wait for a bugfix to BUSCO? Is there another option that I might be missing?

That module is already a horrible mess, what's another strand of spaghetti

You can also skip running bbtools entirely, but if you use batch mode (pass in more than 1 genome) it only gets applied to the first genome..

Would it be an option to add a patch to the conda recipe?

I'm not sure what a sensible patch would be - either we hard-code some new memory number (simple, but if we set it too high it might not work for others), or we make it configurable via command line (probably a serious patch!)

There seems to be a

bbtools_args

https://gitlab.com/ezlab/busco/-/blob/master/src/busco/BuscoConfig.py#L310

I think it's a set of hard-coded options: https://gitlab.com/ezlab/busco/-/blob/master/src/busco/BuscoConfig.py#L71

Perhaps it’s possible to patch the config and a bbtools_mem field that sources it’s value from the environment, with a default fallback?

Perhaps we could just make it add one in here? https://gitlab.com/ezlab/busco/-/blob/master/src/busco/busco_tools/bbtools.py?ref_type=heads#L49

if os.environ.get('BUSCO_BBTOOLS_MEM'):
    bbtools_job.add_parameter(f"--xmx {os.environ.get('BUSCO_BBTOOLS_MEM')}")

yeah sure

Just have to get it past the Bioconda guards... they might not like this

Just ping me 😉

BUSCO already has two

see 😄 we’re not the only ones

Not yet

Approved and merged

Thanks! 🤩