[Bioc-devel] Announcing Docker containers for Bioconductor

[Dan Tenenbaum]

----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> To: "Elena Grassi" <grassi.e at gmail.com>
> Cc: bioc-devel at r-project.org
> Sent: Thursday, January 8, 2015 10:18:50 AM
> Subject: Re: [Bioc-devel] Announcing Docker containers for Bioconductor
> 
> 
> 
> ----- Original Message -----
> > From: "Elena Grassi" <grassi.e at gmail.com>
> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> > Cc: bioc-devel at r-project.org
> > Sent: Thursday, January 8, 2015 8:45:37 AM
> > Subject: Re: [Bioc-devel] Announcing Docker containers for
> > Bioconductor
> > 
> > On Thu, Jan 8, 2015 at 4:43 PM, Dan Tenenbaum
> > <dtenenba at fredhutch.org> wrote:
> > >> 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?
> > 
> > Sorry! It's bioconductor/devel_sequencing image that I had pulled
> > before:
> > data at decoder:~/Dropbox/work/matrix/matrix_rider$ docker images
> > REPOSITORY                      TAG                 IMAGE ID
> >  CREATED             VIRTUAL SIZE
> > bioconductor/devel_sequencing   latest              9f40f8036ad4
> >  29 hours ago        5.715 GB
> > 
> > > 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/
> > 
> > On the second machine this works but on this machine I do not love
> > having this kind of privileges as long as it's shared PC in my
> > office
> > :)
> > What puzzles me it's that the privileges were (i.e. not writable
> > and
> > readable by everyone) the same on both machines and on the first
> > one
> > it has worked from the first moment without a+rw...I assumed that
> > the
> > rstudio user has PID 1000 in the container/image and that -e UID=
> > etc
> > could fix (change it to whatever PID my user has on the host
> > machine)
> > this but this does not seem the case.
> 
> It is not the case. These containers are set up differently than
> Rocker's.
> Though I think I will change them to allow this.
> 
> In the meantime you can accomplish what you want, a bit circuitously.
> Run a command like this:
> 
> docker run -p 8787:8787 -e USER=$USER -e USERID=$UID --rm -it  -v
> /home/data/Dropbox/work/matrix/mr_bioc/matrix_rider/:/opt/matrix_rider
>  bioconductor/devel_sequencing bash
> 
> This opens a shell on the container (as root) where you can do the
> following:
> 
> /tmp/userconf.sh # note different location than on rocker
> # ignore warning that /home/data already exists
> passwd data # choose a passwd for the user, does not have to match
> your real password
> /usr/bin/supervisord
> 
> Then open a browser to http://localhost:8787 and log in with username
> 'data' and the password you just set. You should be able to
> read/write the files in /opt/matrix_rider, assuming you can
> read/write those files when you are logged in as 'data' and _not_
> using docker.
> 
> I will look at doing this in a way more similar to rocker; I'll let
> you know when/if this is done.
> 

You no longer need to do any of the above; the bioconductor containers now behave
like rocker's in this regard (and the web page has been updated accordingly).

You will need to re-pull the image:

docker pull bioconductor/devel_sequencing


Then you should be able to do 

docker run -e USER=$USER -e USERID=$UID -v /home/data/Dropbox/work/matrix/mr_bioc/matrix_rider/:/opt/matrix_rider  -p 8787:8787 bioconductor/devel_sequencing

Then log into Rstudio as user 'data' with password 'rstudio'. And you should be able to read/write the files in /opt/matrix_rider.

Dan