[Bioc-devel] submitting annotation and data package

[Obenchain, Valerie]

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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