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MariaNattestad / Assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
http://assemblytics.com
MIT License
135 stars 28 forks source link

R and Python versions #40

Closed shabirmoosa closed 6 months ago

shabirmoosa commented 3 years ago

Hi,

Could you please provide the versions of R and python used and of the below dependency packages

R ggplot2 plyr RColorBrewer scales

Python argparse numpy

I see an error while running the pipeline and looks like it is coming from the plyr package. Also I'm facing a problem with rendering the plots on the web app installed locally

Thanks Shabir

MariaNattestad commented 3 years ago

Ah yes I've seen issues with R packages for my tutorial videos where code that used to work is not compatible with future versions. I think in Python it's better, once you get to python 3 of course.

Here are the R packages I have installed on my system, which I believe are the ones I had installed last time I ran Assemblytics locally: R: 3.4.0 plyr: 1.8.6 ggplot2: 2.2.1 RColorBrewer: 1.1.2 scales: 1.1.1

Also for Python: Python: 3.7.6 numpy: 1.18.1 argparse: 1.1

Hope that helps! Maria