[Bioc-devel] Announcing Docker containers for Bioconductor

[Radhouane Aniba]

Docker and some bioconductor packages were used long time ago at
CodersCrowd http://coderscrowd.com/ , good to see this move finally hit the
community, awesome move, keep it up

It will be great to support bioconductor users by using CodersCrowd as
well, reproducibility is also when you reproduce errors not just working
code

Cheers

Rad


On Thu, Jan 8, 2015 at 7:43 AM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

>
>
> ----- 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/
>
> Dan
>
>
> >
> > Thanks,
> > E.
> > p.s. sorry Dan for the first mail sent only to you
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
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>



-- 
*Radhouane Aniba*
*Bioinformatics Scientist*
*BC Cancer Agency, Vancouver, Canada*

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