On 29 August 2015 01:19, Martin Morgan wrote: > On 08/28/2015 02:51 PM, Dan Tenenbaum wrote: >> >> >> ----- Original Message ----- >>> From: "Laurent Gatto" <lg...@cam.ac.uk> >>> To: "Dan Tenenbaum" <dtene...@fredhutch.org> >>> Cc: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>, "bioC-devel" >>> <bioc-de...@stat.math.ethz.ch>, "Laurent >>> Gatto" <lg...@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" <kasperdanielhan...@gmail.com> >>>>> To: "Laurent Gatto" <lg...@cam.ac.uk> >>>>> Cc: "bioC-devel" <bioc-de...@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 <lg...@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?
That sounds like a great idea. It would still be nice if Bioconductor kept the topic specific containers (flow, microarrays, proteomics, sequencing). Laurent > Martin > >> Dan >> >> >> Dan >> >>> Laurent >>> >>>> Dan >>>> >>>>>> >>>>>> Best wishes, >>>>>> >>>>>> Laurent >>>>>> >>>>>> _______________________________________________ >>>>>> Bioc-devel@r-project.org mailing list >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioc-devel@r-project.org mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>> >>> >>> >>> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> -- Laurent Gatto | @lgatt0 http://cpu.sysbiol.cam.ac.uk/ _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
