[Bioc-devel] bioconductor singularity images

[Nitesh Turaga]

Hi Poorani,

Thanks for the heads up about this. The "Usage" is auto generated by the 
singularity-hub. But i'm glad that you found a way around it. I'll 
update the instructions on the bioconductor.org website so that it's 
easier to find.

Best,

Nitesh

On 6/15/2020 11:57 AM, Subramanian, Poorani (NIH/NIAID) [C] wrote:
>
> 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.
>
> Sincerely,
>
> 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.
>
>     Best,
>
>     Nitesh
>
>
>
>         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:
>
>         Hello,
>
>         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?
>
>         Thanks!
>
>         Poorani Subramanian, Ph.D.
>         Computational Biology Specialist
>         Contractor, Medical Science and Computing, Inc.
>         Science Support Section
>         Bioinformatics and Computational Biosciences Branch (BCBB)
>         NIH/NIAID OCICB
>         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>
>
>
>         [[alternative HTML version deleted]]
>
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