Question

how can I access my local files (data, R-scripts) from the *docker* R/Bioconductor?

2

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anton.kratz ▴ 60

@antonkratz-8836

Last seen 7 months ago

Japan, Tokyo, The Systems Biology Insti…

I am using R/Bioconductor by invoking

docker run -p 8787:8787 bioconductor/devel_base

and then I point my browser to

http://localhost:8787

to access RStudio.

It works without any problems.

But how can I access my raw data files and R-scripts on my local filesystem? I.e. how can I link my local filesystem to docker?

--

This is under Xubuntu 14.04.3 (xubuntu-14.04.3-desktop-amd64).

docker ubuntu • 2.7k views

ADD COMMENT • link updated 9.1 years ago by Dan Tenenbaum ★ 8.2k • written 9.1 years ago by anton.kratz ▴ 60

score 3 · Accepted Answer · 2015-09-18

3

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Dan Tenenbaum ★ 8.2k

@dan-tenenbaum-4256

Last seen 4 months ago

United States

Read the relevant docker documentation. Also read what rocker has to say about permissions when doing this.

ADD COMMENT • link 9.1 years ago Dan Tenenbaum ★ 8.2k

0

Entering edit mode

Thanks, I could get it to work with this command:

docker run -v $(pwd):/home/rstudio/$USER -p 8787:8787 bioconductor/devel_base

ADD REPLY • link 9.1 years ago anton.kratz ▴ 60