Adding packages to depot.galaxyproject.org

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Adding packages to depot.galaxyproject.org

Peter Cock
Hello all,

How do tool wrapper developers/packagers go about adding entries
to the Galaxy depot? There isn't a GitHub repository for this is there?

Specifically I want to upload some older MIRA releases, e.g. these
URLs have broken, but I have the original files and checksums:

http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mira_4.9.5_2_darwin14.3.0_x86_64_static.tar.bz2
http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mira_4.9.5_2_linux-gnu_x86_64_static.tar.bz2

See also:

https://www.freelists.org/post/mira_talk/Stable-download-URLs-on-sourceforge
https://www.freelists.org/post/mira_talk/MIRA-495-now-missing-on-SourceForge

I'm now running "planemo lint --urls ..." under TravisCI which flags
the broken URLs immediately (rather than finding out when the
installation fails later):

https://github.com/peterjc/galaxy_mira/commit/4e26a4e3f3d69adaab657cb614e56ebcf9968592
https://travis-ci.org/peterjc/galaxy_mira/jobs/150025836

Regards,

Peter
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Re: Adding packages to depot.galaxyproject.org

Eric Rasche-2
Hi Peter,

The cargo port is the ideal place for this, however it does not support manual uploads of files.

On 08. aug. 2016 13:37, Peter Cock wrote:
Hello all,

How do tool wrapper developers/packagers go about adding entries
to the Galaxy depot? There isn't a GitHub repository for this is there?

Specifically I want to upload some older MIRA releases, e.g. these
URLs have broken, but I have the original files and checksums:

http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mira_4.9.5_2_darwin14.3.0_x86_64_static.tar.bz2
http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mira_4.9.5_2_linux-gnu_x86_64_static.tar.bz2
I would recommend the following though others who work on the cargo port might chime in:
  • Upload those tarballs somewhere accessible
  • Add cargo port entries with your URLs

Then cargo port would at least have a copy you can reference in your tools.


See also:

https://www.freelists.org/post/mira_talk/Stable-download-URLs-on-sourceforge
https://www.freelists.org/post/mira_talk/MIRA-495-now-missing-on-SourceForge

I'm now running "planemo lint --urls ..." under TravisCI which flags
the broken URLs immediately (rather than finding out when the
installation fails later):

https://github.com/peterjc/galaxy_mira/commit/4e26a4e3f3d69adaab657cb614e56ebcf9968592
https://travis-ci.org/peterjc/galaxy_mira/jobs/150025836

Regards,

Peter
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--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, Biochemistry & Biophysics
Texas A&M University
College Station, TX 77843
[hidden email]

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Re: Adding packages to depot.galaxyproject.org

Peter Cock
On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche <[hidden email]> wrote:
> Hi Peter,
>
> The cargo port is the ideal place for this, however it does not support
> manual uploads of files.
>

Thanks Eric,

You mean https://github.com/galaxyproject/cargo-port

Is that something which might be addressed in future? The use case
is when a previously public file stops working (either temporarily or
permanently), so you can't use the official URL to make the cached
copy?

Would it be OK to use a short lived URL like a personal dropbox URL,
and then once cached, update urls.tsv with the original official
(but broken) URL?

Peter
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Re: Adding packages to depot.galaxyproject.org

Björn Grüning-3
Hi Peter,

Am 08.08.2016 um 15:54 schrieb Peter Cock:

> On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche <[hidden email]> wrote:
>> Hi Peter,
>>
>> The cargo port is the ideal place for this, however it does not support
>> manual uploads of files.
>>
>
> Thanks Eric,
>
> You mean https://github.com/galaxyproject/cargo-port
>
> Is that something which might be addressed in future? The use case
> is when a previously public file stops working (either temporarily or
> permanently), so you can't use the official URL to make the cached
> copy?
>
> Would it be OK to use a short lived URL like a personal dropbox URL,
> and then once cached, update urls.tsv with the original official
> (but broken) URL?


Yes this is totally fine. We just need to have a way to verify and check
tarballs before upload and we thought github and PR are a nice fit for this.

Thanks,
Bjoern

> Peter
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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>   http://galaxyproject.org/search/mailinglists/
>
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Re: Adding packages to depot.galaxyproject.org

Martin Čech-2
In reply to this post by Peter Cock
Peter:

depot is something we plan on maintaining and providing as a service as long as Galaxy. The cargo-port we will also expand in future (eg to provide dynamic fallback at installation time. It is the right place to put your mira backups (and any other packages you care about in recipes).

Cheers,
M.

On Mon, Aug 8, 2016 at 9:54 AM Peter Cock <[hidden email]> wrote:
On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche <[hidden email]> wrote:
> Hi Peter,
>
> The cargo port is the ideal place for this, however it does not support
> manual uploads of files.
>

Thanks Eric,

You mean https://github.com/galaxyproject/cargo-port

Is that something which might be addressed in future? The use case
is when a previously public file stops working (either temporarily or
permanently), so you can't use the official URL to make the cached
copy?

Would it be OK to use a short lived URL like a personal dropbox URL,
and then once cached, update urls.tsv with the original official
(but broken) URL?

Peter
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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___________________________________________________________
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Re: Adding packages to depot.galaxyproject.org

Peter Cock
In reply to this post by Björn Grüning-3
On Mon, Aug 8, 2016 at 3:27 PM, Björn Grüning <[hidden email]> wrote:

> Hi Peter,
>
> Am 08.08.2016 um 15:54 schrieb Peter Cock:
>> On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche <[hidden email]> wrote:
>>> Hi Peter,
>>>
>>> The cargo port is the ideal place for this, however it does not support
>>> manual uploads of files.
>>>
>>
>> Thanks Eric,
>>
>> You mean https://github.com/galaxyproject/cargo-port
>>
>> Is that something which might be addressed in future? The use case
>> is when a previously public file stops working (either temporarily or
>> permanently), so you can't use the official URL to make the cached
>> copy?
>>
>> Would it be OK to use a short lived URL like a personal dropbox URL,
>> and then once cached, update urls.tsv with the original official
>> (but broken) URL?
>
>
> Yes this is totally fine. We just need to have a way to verify and check
> tarballs before upload and we thought github and PR are a nice fit for this.
>
> Thanks,
> Bjoern

Let's try this then:

https://github.com/galaxyproject/cargo-port/pull/82

(I can't find the Mac binaries for MIRA 4.9.5, hopefully I might have
that on my home machine but it's a long shot.)

Peter
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