search

nanoporetech / pipeline-umi-amplicon

Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
Other
28 stars 10 forks source link

Specify numpy version prevents error #15 #29

Open passelma42 opened 1 year ago

passelma42 commented 1 year ago

Pip install numpy==1.19.5 is not soliving the current dependency issue anymore. Would installing medaka with a python env solve this dependency issue? image

MaestSi commented 9 months ago

Hi @passelma42, I'm facing the same issue too. Do you know why newer numpy versions are causing the issue? Is that due to the fact that they result in the installation of a newer medaka version, with different syntax? SM

passelma42 commented 9 months ago

Hi @MaestSi, Not sure. The way I see it, is that the yml file doesn't specify any version for any of the used dependencies... . Installing the pipeline when it just got out VS installing it today is totally different. For instance, Medaka right now is advised to be installed trough pip in a dedicated pip env, with newer versions not supported any longer through conda (if I remember correctly). This being said, there is another tool out there to analyze UMI's which has been working great for us. Maybe it can be customized to help you out as well: https://doi.org/10.1101/2023.06.19.544637. Greets Pieter

MaestSi commented 7 months ago

Hi @passelma42 , in case you are still interested in the topic, I also wrote a Nextflow implementation of longread_umi pipeline with some adjustments, named UMInator. Best, Simone