error: unable to run rampler!

[mictadlo]

Hi,
I am using Racon v1.3.0. I install it from bioconda. Unfortunately, I got this error:

> racon_wrapper -t 8 ctg_pb.fasta output.gfa1.sam backbone_raw.fasta --split 100000000 > output.racon1.fasta
[RaconWrapper::run] preparing data with rampler
[RaconWrapper::run] error: unable to run rampler!

What did I miss?

Thank you in advance.

Michal

[rvaser]

Hi Michal,
the wrapper problem is probably in the path of rampler when using bioconda (and possibly racon). I'll have to fix this but for the moment you can compile racon locally from github and the wrapper should work.

Best regards,
Robert

[icedevil2001]

I had the same issue. I modified the racon_wrapper with:

9 CONDA_ENV =  os.environ['CONDA_PREFIX']
 10 #*******************************************************************************
 11
 12 class RaconWrapper:
 13
 14     __racon = '{}/bin/racon'.format(CONDA_ENV)
 15     __rampler = '{}/bin/rampler'.format(CONDA_ENV)
 16

Hope that helps.
Best,
Priyesh

[nhartwic]

This still seems to be an issue with bioconda racon, are there any plans for fixing it? Is there a reason it can't be fixed? I don't see why we can't search for rampler at execution time using shutil rather than trying to populate at seemingly compiliation or installation time? I'm not really sure exactly when its getting set.

I'd be happy to submit a pull request for this if it helps.

[nhartwic]

I went ahead and wrote a quick PR. Again, if there is some good reason this isn't already being done, let me know and deny the PR. Honestly, if it were up to me, we would always be looking for rampler in path and doing so would simplify the code a bit, but thats up to you.