Closed cindyeliang closed 2 years ago
Hi @cindyeliang , may i know which sam2tsv you are using?
Hi @Huanle, I was using the sam2tsv provided in the docker image.
I was actually able to get Epinano_Variants to run on the test data already provided in the image's test data directory. However when I tried to run Epinano_DiffErr.R, I now get Rscript: command not found
. Where is R located in this docker image?
Thanks!
Hi @cindyeliang , R command is not included in the docker image.
Hello, I am trying to run the EpiNano test files on the huanleliu/epi12 image on docker. When I initially tried to mount the image onto the directory on my local machine containing the test files (wt.bam, wt.bam.bai, ko.bam, ko.bam.bai, ref.fa, ref.fa.dict, ref.fa.fai), I became unable to view the test files. To get around this, I manually
cp
'd the test files to my docker container.Command used to run Epinano_Variants.py:
python EpiNano/Epinano_Variants.py -R ref.fa -b wt.bam -s sam2tsv.jar -T t -n 6
Error:
When I try to call the Epinano_Variants help dialogue, I get the following:
When I specify using python 3, I do get the help dialogue outputted, but receive this error when running my command instead:
Any help would be appreciated. Thanks!