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
wrote:
> Hello Bioconductor Community,
>
> A quick update about the latest
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
> On Aug 4, 2020,
Hi Robert,
The VCF file uses "22" for the chromosome name which is the name used by
NCBI. So explicitly specifying "hg19" in the readVcf() call is like
saying that this chromosome name is a UCSC name which is why
seqlevelsStyle() gets confused later.
If you specify the name of the NCBI
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
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’)
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 wrote:
> Hi Levi,
>
> Within the RStudio terminal console you
