[Bioc-devel] bioconductor singularity images

Subramanian, Poorani (NIH/NIAID) [C] poor@n|@@ubr@m@n|@n @end|ng |rom n|h@gov
Mon Jun 15 17:57:53 CEST 2020

Thanks, I was able to pull the image just now!  Just a tip for your users on an HPC that don't have root, I couldn't use `singularity run`  as it suggests in the usage<https://singularity-hub.org/collections/3955/usage>.  I think whatever the default run command is requires elevated permissions.  exec and shell work fine to run R, though.  You might also want to link to the Rocker instructions for running with Singularity<https://www.rocker-project.org/use/singularity/> as well.  It's kinda nice to be able to run RStudio Server on an HPC over ssh.


Poorani Subramanian, Ph.D.
Computational Biology Specialist, BCBB Science Support
Contractor, MSC, Inc.
Office: 240.747.7378 | Mobile: 301.875.8573
bioinformatics @NIAID<https://bioinformatics.niaid.nih.gov/services>

From: Nitesh Turaga <nturaga.bioc using gmail.com>
Date: Monday, June 15, 2020 at 11:11 AM
To: Poorani Subramanian <poorani.subramanian using nih.gov>
Cc: "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] bioconductor singularity images

Please check https://singularity-hub.org/collections/3955

On Jun 15, 2020, at 11:09 AM, Nitesh Turaga <nturaga.bioc using gmail.com<mailto:nturaga.bioc using gmail.com>> wrote:

Yes we do.

You should see it in about 1 hour. It should have been available. My bootstrap file to convert the docker image to singularity had an extra newline character which prevented the build.

Thanks for spotting this. I’ve made the fix.



On Jun 15, 2020, at 10:56 AM, Subramanian, Poorani (NIH/NIAID) [C] via Bioc-devel <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>> wrote:


I see you have provided bioconductor singularity images<http://bioconductor.org/help/docker/#singularity> for release 3.10<https://singularity-hub.org/collections/3955>.  Do you have any plans to do the same for 3.11?


Poorani Subramanian, Ph.D.
Computational Biology Specialist
Contractor, Medical Science and Computing, Inc.
Science Support Section
Bioinformatics and Computational Biosciences Branch (BCBB)
Building 31, Room 3B62, 31 Center Drive, Bethesda, MD 20814
Office: 240.747.7378 | Mobile: 301.875.8573
bioinformatics @NIAID<https://bioinformatics.niaid.nih.gov/services>

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