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[Bioc-devel] bioconductor_docker updates

6 messages · Turaga, Nitesh, Levi Waldron, Sean Davis +1 more

Turaga, Nitesh
# 
Hello Bioconductor Community,

A quick update about the latest developments on the Bioconductor Docker images.

We have updated the ?devel? image to inherit from the latest ?rocker/rstudio:4.0.2? image. This means that the `bioconductor/Bioconductor_docker:devel` image, which is now available will be running on,


  1.  Ubuntu 20.04
  2.  R version 4.0.2
  3.  Bioconductor version 3.12.

One major update to the system requirements was the installation of the ?libglpk-dev? which seemed to have caused issues installing the ?igraph? package. The version number of this image which can be queried through the docker command is going to be 3.12.13.

If you pull the updates from dockerhub using,

          docker pull bioconductor/Bioconductor_docker:devel

And check the version number using, (the result is going to be 3.12.13.

           docker inspect --format '{{ index .Config.Labels.version}}' bioconductor/bioconductor_docker:devel


NOTE: The release image stayed exactly the same but with the addition of the `libglpk-dev` package. The RELEASE_3_11 image did not get updated to Ubuntu 20.04. It is still based on Ubuntu 18.04. The devel image now works on a different version of Ubuntu (20.04) as compared to the build system (18.04. The support for the 18.04 image on rocker is no longer available.

The inspect label command for  RELEASE_3_11 (given below) should produce the new version number 3.11.11. Do not forget to pull. This is a bug fix with regards to the igraph package?s missing dependency.

docker inspect --format '{{ index .Config.Labels.version}}' bioconductor/bioconductor_docker:RELEASE_3_11


If you have any further questions, please reply to this thread.

Best regards,

Nitesh Turaga
Bioconductor Core Team


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Levi Waldron
# 
Thanks Nitesh! Very much appreciated. I was wondering, is there a way to
inspect the version from _within_ the image, i.e., that could supplement a
sessionInfo() command?

On Mon, Aug 3, 2020 at 6:30 PM Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>
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      Nitesh Turaga
    

    

      
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Hi Levi,

Within the RStudio terminal console you can check the contents of the file `/etc/environment`. This should show you a version number 

$ cat /etc/environment
?BIOCONDUCTOR_DOCKER_VERSION = 3.11.11'

(The example above is run on a RELEASE_3_11 image)

Best,

Nitesh

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Sean Davis
    

    

      
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Thanks for operationalizing some of the recent lessons in dockerworld,
Nitesh! Is there a place to start discussing how to implement tests for
these images, or is that premature?

Sean

        
On Tue, Aug 4, 2020 at 6:33 AM Nitesh Turaga <nturaga.bioc at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Nitesh Turaga
    

    

      
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Hi Sean,

I think either this email thread or the #containers channel on the community-bioc slack is the best place to discuss implementation of integration tests for these images. 

I?m doing some proof-of-concept preliminary work on the integration tests in the next 3 weeks, but I?d say it?s not pre-mature to discuss them. 

I might have a better sense of what is possible/what is not, in 2-3 weeks time. But I?m open to discussion. 

Best,

Nitesh

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Nitesh Turaga
    

    

      
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Hi Levi,

Just wanted to follow up on this again, I?ve made a few changes to the 3.12.14 image version on the `bioconductor/bioconductor_docker:devel` image, where you should be able to query for the version _within_ the docker image using,

	Sys.getenv(?BIOCONDUCTOR_DOCKER_VERSION?)

This is a much easier way of interacting with the environment variable. 

And if you want to get a sense of what is the current version number of the ?devel? image hosted on Dockerhub, instead of looking up the image version on Github each time, you could use my little package function. This works on your local machine _outside_ the docker container. (I?m planning on extending the functionality of BiocDockerManager::version() to work _within_ the docker image as well)

	> BiocDockerManager::version(repository=?bioconductor/bioconductor_docker?, tag = ?devel?)
	[1] ?3.12.14"

Best,

Nitesh