Comments (5)
I changed it to git+https://github.com/rrwick/Porechop.git
and the conda completed. Let's see if the rest of the instructions work...
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Just linking this comment here for reference.
The download links for the models and singularity image have been updated.
As above, if you remove the porechop dependancy from the scripts/herro-env.yml
it will build - this fork of porechop no longer exists plus porechop is not needed if you have used a recent version of Dorado to process your data (as commented in the README):
In Dorado v0.5, adapter trimming was added, so adapter trimming and splitting using Porechop and duplex tools will probably be removed in the future.
Additionally Herro error correction has just been integrated into the Dorado basecaller: https://github.com/nanoporetech/dorado?tab=readme-ov-file#read-error-correction
from herro.
I think that i have the same issue
L
from herro.
Neither the sif nor the models are available because http://complex.zesoi.fer.hr
is down. EDIT! I did eventually get it compiled but it crashed. Hopeful for the next version.
from herro.
I close this issue since there are multiple suggested solutions by now:
- compile without Porechop
- run via ONT's dorado >= v0.7.0
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Related Issues (20)
- Memory errors? HOT 3
- Out of bounds for 2-bit sequence decoding. HOT 2
- Observation: Reads get split at certain intervals more often. HOT 3
- hifiasm options HOT 1
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- Poor assembly metrics with hifiasm v0.19.8
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- model training
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