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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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how to make CNVkit use a defined local Version of R/ Rscript in a local install #757

Closed claus-h-g closed 1 year ago

claus-h-g commented 1 year ago

Hi, many thanks for providing CNVkit.

On xUbuntu 18.04 I would like to use a local installaton of CNA kit not using the local preinstalled system R but a R version I did install in addition to the existing one, so I can run a version pinning without (hopefully) affecting any other analysis steps on this machine. After following the instruction for a local installation git clone https://github.com/etal/cnvkit cd cnvkit/ pip install -e . and the installation of dependencies,

I did adjust the Makefile in /cnvkit/test so the correct Rscipt is used. After running make The test completed without any error message.

How do I transfer the modifications to the Makefile to the CNVkit config for analyzing real samples?

claus-h-g commented 1 year ago

A friend suggested to expand the $PATH in the activate for my Python virtual (!= conda) environment. That seems to do the trick. sorry for posting

whiffen-cann commented 1 year ago

add the path of Rscript to your $PATH，for my conda installtion , it's same as the path of cnvkit.py .For example,whent I execute my cnvkit.py ,I execute " export PATH=/data1/software/install-miniconda3/envs/cnvkit/bin/:$PATH "