Comments (3)
Overall, I was also wondering if it wouldn't be simpler to provide a pre-built Singularity image?
There is one linked in the README 😉
https://github.com/lbcb-sci/herro?tab=readme-ov-file#installation
wget http://metals.zesoi.fer.hr:9080/herro/herro.sif
from herro.
Thanks for pointing this out, turns out I have been confused by the order of the steps in the README (a, b, c, etc.) where I thought I needed to download herro.sif first and then, do some more singularity building afterwards. After more careful reading, I understand now I can just download the image and that's it.
I guess I don't have to do the condo env create
then but the problem still stands for those who would want to.
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I'm not sure what the issue is with your environment creation, I just tested on my local machine and a remote linux server and both built successfully after I removed the porechop dependancy from the scripts/herro-env.yml
- 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. I imagine the devs will remove the porechop dependancy in the near future:
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
Edit: you might need to look at your conda set up, I see the required versions of things like tk
:
$ conda search -f tk
Loading channels: done
# Name Version Build Channel
tk 8.5.19 0 conda-forge
tk 8.5.19 1 conda-forge
tk 8.5.19 2 conda-forge
tk 8.6.6 0 conda-forge
tk 8.6.6 1 conda-forge
tk 8.6.6 2 conda-forge
tk 8.6.6 3 conda-forge
tk 8.6.6 4 conda-forge
tk 8.6.6 5 conda-forge
tk 8.6.7 0 conda-forge
tk 8.6.7 h5979e9b_1 pkgs/main
tk 8.6.7 hc745277_3 pkgs/main
tk 8.6.8 0 conda-forge
tk 8.6.8 h84994c4_0 conda-forge
tk 8.6.8 h84994c4_1000 conda-forge
tk 8.6.8 ha92aebf_0 conda-forge
tk 8.6.8 hbc83047_0 pkgs/main
tk 8.6.9 h84994c4_1000 conda-forge
tk 8.6.9 h84994c4_1001 conda-forge
tk 8.6.9 ha92aebf_0 conda-forge
tk 8.6.9 hed695b0_1002 conda-forge
tk 8.6.9 hed695b0_1003 conda-forge
tk 8.6.10 h21135ba_1 conda-forge
tk 8.6.10 hbc83047_0 pkgs/main
tk 8.6.10 hed695b0_0 conda-forge
tk 8.6.10 hed695b0_1 conda-forge
tk 8.6.11 h1ccaba5_0 pkgs/main
tk 8.6.11 h1ccaba5_1 pkgs/main
tk 8.6.11 h21135ba_0 conda-forge
tk 8.6.11 h27826a3_1 conda-forge
tk 8.6.12 h1ccaba5_0 pkgs/main
tk 8.6.12 h27826a3_0 conda-forge
tk 8.6.13 h2797004_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tk 8.6.13 xft_h2e05e87_1 conda-forge
tk 8.6.14 h39e8969_0 pkgs/main
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Related Issues (20)
- Memory errors? HOT 3
- Installation issues during conda env create HOT 5
- 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
- CLR read model training HOT 1
- HERRO's 10Kb input recommendation HOT 1
- Poor assembly metrics with hifiasm v0.19.8
- Core dumped at herro inference HOT 4
- Models inaccessible HOT 6
- model training
- How to reduce RAM usage of "herro inference"? HOT 2
- location of scripts in singularity container
- Downloading Data failure and QV calculation
- how to install herro without root HOT 1
- Question Regarding Error Rate Evaluation Using bamConcordance
- `RUST_BACKTRACE=1`
- Download of Singularity image (current link is dead) HOT 1
- RUST_BACKTRACE=1 HOT 3
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