Re: [galaxy-dev] Implementing iRODS with Galaxy

[Katherine Beaulieu]

Well I guess this didn't reply to the post I wanted, sorry everyone!

On Mon, Jul 18, 2016 at 6:50 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Hi there,
> I have developed a tool that does the importing and exporting to Galaxy.
> Please see the attached link to the github repos for the two tools.
> Please keep in mind that this tool is still in development. As well, it
> has only been tested on a local instance of Galaxy and the authentication
> with iRODS has not quite been worked on. If you have any suggestions please
> let me know.
>
>
> https://github.com/AAFC-MBB/Galaxy/tree/dev/wrappers/irods_pull
> https://github.com/AAFC-MBB/Galaxy/tree/dev/wrappers/irods_push
>
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[galaxy-dev] Implementing iRODS with Galaxy

[Katherine Beaulieu]

Hi there,
I have developed a tool that does the importing and exporting to Galaxy.
Please see the attached link to the github repos for the two tools.
Please keep in mind that this tool is still in development. As well, it has
only been tested on a local instance of Galaxy and the authentication with
iRODS has not quite been worked on. If you have any suggestions please let
me know.


https://github.com/AAFC-MBB/Galaxy/tree/dev/wrappers/irods_pull
https://github.com/AAFC-MBB/Galaxy/tree/dev/wrappers/irods_push
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Re: [galaxy-dev] Implementing iRODS with Galaxy

[Peter van Heusden]

Hi Miuki

There's two aspects to iRODS and Galaxy. Firstly, there is the Galaxy
object store which can store objects in iRODS. This is entirely hidden from
the user and they have no idea that their datasets are in iRODS. Some work
on that happened earlier in this year, see:

https://wiki.galaxyproject.org/Community/Log/2015/GalaxyIrodsConnection

Then there is the question of iRODS import/export. See this thread from
earlier this year: http://dev.list.galaxyproject.org/iRODS-td4669076.html -
Iyad Kandalaft (http://www.goc411.ca/en/8192/Iyad-Kandalaft) mentioned some
future work on import/export. As part of the B3Africa project some
colleagues of ours are also investigating iRODS import/export. I think it
might be useful to make a GitHub issue describing the problem and have
people comment on there.

I had a brief look at the iRODS python client library and it seems to be in
a relatively early state of development (
https://github.com/irods/python-irodsclient) but it is definitely usable.

On 29 June 2016 at 21:40, Yip, Miu ki  wrote:

> Hello Galaxy Team,
>
> We're from the Bioinformatics Shared Resources (BSR) at Cold Spring Harbor
> Labs and we're looking to implement irods on a newly installed version of
> Galaxy.
>
> We want to incorporate iRODS (http://irods.org/). Is there a recommended
> way to do this, or no?
>
> Thanks in advance for the advice.
>
> Best,
> Miuki Yip
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