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wenbostar / PGA

PGA: a tool for ProteoGenomics Analysis
http://wenbostar.github.io/PGA/
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rTANDEM is unavailable #25

Closed zhangyimin40 closed 2 years ago

zhangyimin40 commented 2 years ago

Hi,

I failed to install PGA as rTANDEM has been removed from bioconductor, could you please let me know the solution?

Bioconductor version 3.12 (BiocManager 1.30.16), R 4.0.4 (2021-02-15) Installing package(s) 'rTANDEM' package �rTANDEM� is not available for Bioconductor version '3.12'

Thanks

wenbostar commented 2 years ago

You could use an older version of Bioconductor as shown here: https://github.com/wenbostar/PGA/blob/docker/Dockerfile.

In addition, you could use our prebuilt docker of PGA: docker pull proteomics/pga

zhangyimin40 commented 2 years ago

Thanks Bo, it's resolved!

BenSamy2020 commented 2 years ago

Greetings @wenbostar,

I came across this extremely useful package of yours. Unfortunately, I am facing this similar issue. So I performed the docker pull proteomics/pga command and successfully installed it. I am extremely new to command line. By any chance do you have a guide on how to run this program using docker? Additionally, how do you integrate RStudio into this environment for usage?

Regards, Ben

wenbostar commented 2 years ago

Could you open a new issue and describe what function in PGA you want to use?

BenSamy2020 commented 2 years ago

Greetings @wenbostar,

My apologies for the inconvenience caused. I have created a new issue.

Regards, Ben

wenbostar commented 2 years ago

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