get_parameter no longer used in pyPiper

[rcorces]

Hey @nsheff - I was in need of an RNA-seq pipeline and I naturally came here. I went with the Kallisto version since it was the most-recently updated (good idea or bad idea?). I'm not sure if you guys are still maintaining these. Getting this up and running was very smooth with the exception of the following issue:

I think get_parameter is no longer used in the newer version of pyPiper. It was changed to get_first_value via databio/pypiper@62cc784. At least in the Kallisto pipeline this needs to be changed in the following places:

rnapipe/src/rnaKallisto.py

Line 12 in 42ff6b1

from pypiper import add_pypiper_args, get_parameter, NGSTk, PipelineManager

and

rnapipe/src/rnaKallisto.py

Line 213 in 42ff6b1

getopt = partial(get_parameter, param_pools=[sample, cmdl_opts, pipe_opts])

I did not find uses of get_parameter in the other pipelines, perhaps because they arent really used?

[nsheff]

I'd say we are still maintaining these, but we do less stuff with RNA so they are less used... but the kallisto one should work for you, if kallisto is what you want to use.

Yeah -- get_parameter is a really useful thing but it wasn't widely used yet -- it looks like we missed this use of it when we made the name change.

I've updated it now here in rnapipe...

[nsheff]

by the way, FYI there's a new version of pypiper out just a week or two ago:

http://code.databio.org/pypiper/changelog/

and within the next week we will have a new release of looper, peppy, and caravel:

pepkit/looper#152

pepkit/peppy#260

pepkit/caravel#67

So you might want to check those out, early next week

[rcorces]

awesome!

[nsheff]

did that work for you?

[rcorces]

yep