Ability to use a particular package via Docker
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@jordanxanthopoulos-11527
Last seen 4.4 years ago

Hi, I just started using docker and I what I want to know is if I can actually download with a command a particular package, with its dependencies,inside the Dockerfile, instead of dl'ing the whole category, cause it makes my image too big for no reason.

What I am doing at the moment is just adding: FROM bioconductor/release_flow in the top of the docker file.

The problem is, I only need the flowcore library, which is part of the flow release. I tried running this command, from somewhere else:

RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("flowCore", dep = TRUE)'

but I got some errors, since some dependencies failed to install, rendering the image useless.

Docker flowcore dockerfile • 948 views
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Please post the `sessionInfo` and error message.

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http://imgur.com/a/qiUHx

These are the final lines. Note that the only steps I have are, adding the rocker/shiny, adding some CRAN libraries (successfully) and then running this line to get my bioconductor package.

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Can you also show the errors during  `XML` and `ncdfFlow` installations? Without these information, my best guess is some `C` libraries are missing  (e.g. libxml2 and hdf5)

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http://imgur.com/a/7DOJM

I managed only to catch the XML. Can you understand what the problem may be? I can see the libxml2 is indeed missing. How can I add this via the dockerfile?

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You need to install libxml2 library.

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I fixed the XML problem. There are more problems to be solved though. The HDF5 package is no longer on CRAN. What am I supposed to do?

http://imgur.com/a/aHFcM

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As I said, you need c library for hdf5. The same for GL.

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Hey, thank you for the replies. I've come up with more questions.

RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("flowCore", dep = TRUE)'

what i have added to the rocker dockerfile are these C libraries
libxml2-dev \
    libxml2 \
    mesa-common-dev \
    libglu1-mesa-dev \ 
    freeglut3-dev \
    hdf5-tools \
    libhdf5-openmpi-dev \
    libhdf5-serial-dev 
needed for various packages from CRAN or bioconductor. Still, I get a warning about the rgl http://imgur.com/a/QQ7Bx (no errors though) and when I try to run a simple container i get this
"standard_init_linux.go:175: exec user process caused "exec format error". I am guessing this has to do something with the rgl error I posted.

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libhdf5-openmpi-dev and hdf5-tools are not necessary.

I don't know how to resolve the dock container issue through. Maybe you should install the flowCore directly to your linux instead of through docker.

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yeah, the thing is I want to have a ready-to-go image of my R app for anyone, not just locally. Thanks for the replies. I am closing the thread

 

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