[Bioc-devel] submitting annotation and data package

[Obenchain, Valerie]

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

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]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>> _______________________________________________
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>> 	[[alternative HTML version deleted]]
>>
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