[Bioc-devel] submitting annotation and data package

[Kasper Daniel Hansen]

I can do that (when Im done in a day or two), but just wanted to add that
right now I have my annotation / data packages on Bitbucket which has some
of the same advantages as Github but does not have a 100MB limit on files
(in effect it has a similar 1-2GB limit on repo size).  That would allow
review to be done as issues / etc, but there is no integration with the
build system.

Best,
Kasper


On Wed, Jun 15, 2016 at 10:52 AM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:

> On 06/15/2016 07:33 AM, Obenchain, Valerie wrote:
> > Hi,
> >
> > Historically annotation packages were not reviewed in the package
> > tracker. Last year I starting asking authors to upload the package to a
> > S3 bucket and open an issue on the package tracker (with no upload). I
> > reviewed the package and posted comments to the tracker. This kept all
> > communication in one place and gave us a record of approved packages. It
> > doesn't sound like this system will work with the new tracker.
> >
> > For annotation and large experimental data packages maybe we need an
> > option to create an issue without an associated github repo? Or at least
> > a flag that prevents a commit from kicking off a new build (would fail
> > if data are in S3/dropbox/etc. and only software is in github).
> >
> > This separation of data and software is not a problem with resources
> > contributed to ExperimentHub. Data are permanently stored in S3 and the
> > parent software package submitted to the tracker uses ExperimentHub() to
> > load the data.
> >
> > Kasper, if your package is annotation and not experimental data and you
> > want it as a package instead of in AnnotationHub please upload to this
> > S3 bucket
> >
> >   aws --profile username s3 cp dataobject
> > s3://contributed-annotation-experiment/myannotationpackage --acl
> public-read
>
> Sorry, the 'cp' part was confusing, this should have read:
>
> aws --profile username s3 cp myannotationpackage
> s3://contributed-annotation-experiment/myannotationpackage --acl
> public-read
>
> Val
>
>
> >
> > and I'll start the review from there. If you'd rather put the data in
> > AnnotationHub I can help with that too.
> >
> > Val
> >
> >
> >
> > On 06/15/2016 05:01 AM, Martin Morgan wrote:
> >> On 06/14/2016 10:10 PM, Kasper Daniel Hansen wrote:
> >>> In my case its an annotation package thats >100MB.  But I could imagine
> >>> experiment package doing that as well.
> >> very large packages don't play well with SVN or the repository, e.g.,
> >> placing storage burden on repository mirrors. ExperimentHub might be a
> >> better, emerging, solution...
> >>
> >> Martin
> >>
> >>> On Tue, Jun 14, 2016 at 10:08 PM, Dan Tenenbaum <
> dtenenba at fredhutch.org>
> >>> wrote:
> >>>
> >>>> Actually, here is the process for experiment packages:
> >>>>
> >>>>
> >>>>
> https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#submitting-related-packages
> >>>>
> >>>> Not sure what to do if there is a file > 100MB. There is git/github
> large
> >>>> file storage but we don't explicitly support it.
> >>>> Maybe it belongs in ExperimentHub instead?
> >>>>
> >>>> Dan
> >>>>
> >>>>
> >>>> ----- Original Message -----
> >>>>> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> >>>>> To: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> >>>>> Cc: "bioc-devel" <bioc-devel at r-project.org>
> >>>>> Sent: Tuesday, June 14, 2016 7:02:25 PM
> >>>>> Subject: Re: [Bioc-devel] submitting annotation and data package
> >>>>> For annotation packages, see this:
> >>>>>
> >>>>>
> >>>>
> https://bioconductor.org/developers/package-submission/#annotation-packages
> >>>>> For experiment packages, I'm not sure.
> >>>>>
> >>>>> Dan
> >>>>>
> >>>>>
> >>>>> ----- Original Message -----
> >>>>>> From: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> >>>>>> To: "bioc-devel" <bioc-devel at r-project.org>
> >>>>>> Sent: Tuesday, June 14, 2016 6:28:06 PM
> >>>>>> Subject: Re: [Bioc-devel] submitting annotation and data package
> >>>>>> Also, just a point, GitHub does not allow files >100MB.  That is a
> >>>>>> non-issue (I hope) for software packages, but could be hit by
> annotation
> >>>>>> packages, including one I maintain
> >>>>>>
> >>>>>> On Tue, Jun 14, 2016 at 8:53 PM, Kasper Daniel Hansen <
> >>>>>> kasperdanielhansen at gmail.com> wrote:
> >>>>>>
> >>>>>>> Should I submit a new annotation and a new data package through
> the new
> >>>>>>> GitHub interface, or use something differently?
> >>>>>>>
> >>>>>>> Best,
> >>>>>>> Kasper
> >>>>>>>
> >>>>>>       [[alternative HTML version deleted]]
> >>>>>>
> >>>>>> _______________________________________________
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> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>> _______________________________________________
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> >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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