[Bioc-devel] Dependencies in Bioconductor dockers

On 08/28/2015 02:51 PM, Dan Tenenbaum wrote:

----- Original Message -----

From: "Laurent Gatto" <lg390 at cam.ac.uk>
To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
Cc: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>, "bioC-devel" <bioc-devel at stat.math.ethz.ch>, "Laurent
Gatto" <lg390 at cam.ac.uk>
Sent: Friday, August 28, 2015 2:28:29 PM
Subject: Re: [Bioc-devel] Dependencies in Bioconductor dockers


On 28 August 2015 20:42, Dan Tenenbaum wrote:

----- Original Message -----

From: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
To: "Laurent Gatto" <lg390 at cam.ac.uk>
Cc: "bioC-devel" <bioc-devel at stat.math.ethz.ch>
Sent: Wednesday, August 26, 2015 2:36:08 PM
Subject: Re: [Bioc-devel] Dependencies in Bioconductor dockers

This might be especially nice if we use the docker containers for
R
CMD
check.

In this case, you would be checking your own package, right, so the
docker image cannot know in advance what the Suggests dependencies
of
your package are.

[More below].

On Wed, Aug 26, 2015 at 10:56 PM, Laurent Gatto <lg390 at cam.ac.uk>
wrote:

Dear all,

As far as I can see, the Suggests dependencies of a package are
not
included in the docker containers. Would you consider adding
these?
It
would be nice to be able to run all examples and vignette code
of
the
packages available in a container.

Adding the Suggests dependencies of all packages installed on the
image is going to make the image much bigger. This request comes
soon
after other requests to reduce the size of the images. We should
probably have a wider discussion and decide exactly what type of
docker images we want to have.

Use cases that have been mentioned are:

   - an image for building/checking with travis (sounds similar to
     Kasper's request above).  For this one in particular, small
     size is
     important as Travis has to build its environment from scratch
     every
     time, and loading large images takes too long.
   - an image that has the Suggests dependencies of all installed
     packages installed.

We might want to pick a different way to decide what packages are
installed on a given image.  Currently we install all packages with
a
given biocView (Sequencing for example) and this leads to very
large
images (sequencing = ~7.5GB).

Thank you for these clarifications, Dan.

If there is interest in having full/complete containers in addition
to
requiring light ones, would it make sense to distribute both? Would
that
be much overhead?

I think it definitely makes sense to distribute the light containers. (and even then, I want to see how small a 'light' container is--one that contains R, LaTeX, and every system dependency that we know about)
I am a little hesitant to make the existing bloated containers even bigger by adding all the Suggests dependencies. That's why I said we might want to revisit the way we decide what packages are on a given container. Right now we use biocViews (Microarray, Sequencing, Proteomics, FlowCytometry) but that results in huge containers containing many packages that people arguably don't use that much but just happen to have the correct biocView. Of course it does have the benefit of being a somewhat democratic method.

I don't really know what I'm talking about, but does it make sense to think of 
the docker images provided by Bioconductor as building blocks for more 
specialized containers? i.e., that it should not be 'hard' for a developer to 
make an image that is appropriate for their particular needs?

It seems like there's value to some level of nimbleness provided by small 
container size. I also wonder about LaTeX -- it seems like HTML vignettes are 
way better, and since docker images are forward-looking, maybe the images should 
be provisioned with the notion that they'll support HTML?

Maybe there could be a docker-factory script that would take the name of a base 
image and the path to a package repository, and create a derived image with the 
additional necessary dependencies?

Martin

Dan


Dan

Laurent

Dan

Best wishes,

Laurent

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