[Bioc-devel] Multiple projects for submission to Bioconductor

Brian Schilder br|@n_@ch||der @end|ng |rom @|umn|@brown@edu
Tue Jan 3 11:21:20 CET 2023

Hi Ali,

I�d just like to add that biocthis is great if you�d like to have use static workflow file. But if you�re looking for something that is centrally maintained (ie an action) without you having to update your workflow file each time there�s an update or bug fix, you can use rworkflows:


From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Ali Sajid Imami <ali.sajid.imami using gmail.com>
Date: Tuesday, 3 January 2023 at 04:07
To: Vincent Carey <stvjc using channing.harvard.edu>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>, Ali Sajid Imami <Ali.Imami using rockets.utoledo.edu>
Subject: Re: [Bioc-devel] Multiple projects for submission to Bioconductor

Thank you for the detailed response. I�ll make sure I dot all the I�s and
cross all the T�s. I�ll also reach out to the author of Biocthis to cross
verify things.

Looking forward to the submission process and thank you and the
bioconductor team for this amazing service.

On Mon, Jan 2, 2023 at 8:12 PM Vincent Carey <stvjc using channing.harvard.edu>

> On Mon, Jan 2, 2023 at 7:51 PM Ali Sajid Imami <ali.sajid.imami using gmail.com>
> wrote:
>> Hi Colleagues,
>> I am currently a PhD student in Bioinformatics at the University of
>> Toledo,
>> College of Medicine and Life Sciences. I am working in the cognitive
>> disorders research lab (https://cdrl-ut.org) and we have been actively
>> developing multiple packages. We are particularly interested in
>> building data and analysis packages for Kinase Activity analysis.
>> We have a number of packages that we would like to submit to Bioconductor
>> for acceptance. I am currently in the process of streamlining the
>> packages,
>> making sure their dependencies are clearly defined and extracting large
>> datasets into their own data packages.
>> I had a couple of questions regarding the submissions:
>> 1. At our lab we rely heavily on Github Actions for continuous integration
>> and delivery. Are the actions outlined in the biocthis (
>> https://bioconductor.org/packages/release/bioc/html/biocthis.html)
>> package
>> up to date and something we can reliably build on?
> Thank you for your note.
> I would say the answer here is "yes", but you could also check with the
> author of biocthis to see whether there are any concerns to be aware of.
>> 2. We have quite a few packages and there may be some packages that would
>> be better to go into the same release. Is it possible to submit them all
>> separately but have their review process be streamlined, collectively?
> It is impossible to say without more information.  We have limited
> personnel
> for reviewing.  There is an approach for submitting related packages, see
> here
> <https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#submitting-related-packages>
> .
> 3. Is Bioconductor's git infrastructure set up to update from our github
>> repo or is there a solution we can build to push our new "release" to the
>> bioconductor git infra after the integration tests in github actions are
>> completed?
> I suspect you could accomplish update-git-on-push-to-github but perhaps
> further discussion is needed.  At this time our build system works with git
> repositories that are jointly managed by us and by the package maintainer.
> Maintainers are responsible for ensuring that the git repository is up to
> date.
> Sincerely,
> Vincent Carey
>> Thank you.
>> Regards,
>> Dr. Ali Sajid Imami
>> LinkedIn <https://pk.linkedin.com/pub/ali-sajid-imami/50/956/2a6>
>>         [[alternative HTML version deleted]]
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