[Bioc-devel] Announcing Docker containers for Bioconductor

Dan Tenenbaum dtenenba at fredhutch.org
Thu Jan 8 16:43:35 CET 2015

----- Original Message -----
> From: "Elena Grassi" <grassi.e at gmail.com>
> To: bioc-devel at r-project.org
> Sent: Thursday, January 8, 2015 5:11:50 AM
> Subject: Re: [Bioc-devel] Announcing Docker containers for Bioconductor
> Thanks, this is really useful and I was looking forward to it after
> having used rocker!
> I have a strange (ok, at least to me :) ) issue concerning volumes.
> On a machine (debian testing/unstable up to date) everything works
> smoothly when I do something like:
> data at decoder:~$ docker run -v
> /home/data/Dropbox/work/
> matrix/mr_bioc/matrix_rider/:/opt/matrix_rider
> -p 8787:8787 9f40f8036ad4
> (in /home/data/Dropbox/work/matrix/mr_bioc/matrix_rider/ I have a
> Rstudio project)

What image is 9f40f8036ad4? Why are you not using the user/repository name for the image? Is it a rocker image or a Bioconductor image?

> The same command on another machine (more or less the same debian as
> before) leads me to being unable to open the project with Rstudio as
> long as the directory is not writeable.
> The only relevant difference seems to be my user UID which is 1000 on
> the first machine but different on the other one. I tried to use -e
> as
> suggested here
> https://github.com/rocker-org/rocker/wiki/Sharing-files-with-host-machine
> with no luck.
> Does anyone more docker-savy than me have a suggestion? (maybe the
> volumes approach is not the best one here).

Note that Rstudio Server runs as a user called rstudio, not necessarily a privileged user.
So the directory you are trying to mount should probably be writable (and readable) by all.
so try 

chmod -R a+rw /home/data/Dropbox/work/matrix/mr_bioc/matrix_rider/


> Thanks,
> E.
> p.s. sorry Dan for the first mail sent only to you
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