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hey guys! i am trying to test out parabricks/starf...
# modules
a
hey guys! i am trying to test out parabricks/starfusion and got an odd error:
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usage: pbrun starfusion <options>
Help: pbrun starfusion -h
pbrun: error: unrecognized arguments: --num-gpus 1
this is not an option i added, it is hard-coded into the module when using gpu acceleration. seems like i have to use --num-threads 1 instead. it seems very odd to me if this is a real error and the module passed checks, and from what i can see it looks like it was configured to run on gpu runners. it also seems odd to me that this module hasn't been edited in a year without anyone noticing? just wondering if there's something wrong with my setup is all
in the nf-test config: github.com/nf-core/modules/blob/…/nextflow.config the accelerator is set only for PARABRICKS_RNAFQ2BAM but not PARABRICKS_STARFUSION. i think this explains why there was no error in the nf-test, because --num-gpus is not set without the accelerator turned on. but why wouldn't we want the accelerator turned on and controlling at least num-threads?
just figured out that starfusion is not actually gpu accelerated 😄
s
> just figured out that starfusion is not actually gpu accelerated But why is it in parabricks then? confused dog
f
Because its needed for version compatability
@Gary Burnett can probably tell you more
(if I remember this correctly)
but the pbrun error actually confuses me
a
you absolutely could use regular star-fusion but the burden is on the developer to figure out exactly what's compatible with the parabricks aligner. The parabricks starfusion caller offers a "one-stop-shop" for the user.
but considering i have to locate the correctly versioned starfusion reference anyways, i'm not sure it's adding that much.
g
Hi everyone, I am back from a short PTO. Apologies in my delay for responding. Parabricks starfusion is accelerated on the CPU, but not fully ported to the GPU. @Anne Marie Noronha are you able to run Parabricks star-fusion now? I can make a note in the module docs that starfusion is a CPU based tool to prevent errors like this in the future. Also, for locating starfusion reference, would it be helpful for me to include a link in the modules docs as well? In creating this module, I was hoping to make it easy for end users to run the correct version, so this is already great feedback that there is still some friction here. Thank you!
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