Dear all,
I have Galaxy server which is completely seprated to the Data storage.
I would like to cimmunicate with IRODs for data handling. Thank to Mikael
from URGI, with his pdf about the connexion they made at URGI, I know
better how to make it.
But I have a problem, I would like to use the env (user name + permissions)
of the user who is connecting to Galaxy to pick up the data.
I don't want to retrieve data as Galaxy but by the user name / permissions.
Do you think that it is possible to source the env of eache user and ask
Galaxy to connect as the user and get the data ?
Thanks in advance,
Mohamed
2016-03-11 15:47 GMT+01:00 Mikael Loaec <mikael.loaec(a)versailles.inra.fr>:
Hi,
We put online the pdf file about Galaxy and iRODS connexion on our site.
You can find it here :
https://urgi.versailles.inra.fr/Tools/Galaxy
in Admin corner section.
I also send the form for Galaxy Community Log Board.
If iRODS team wants to host the file, you can do it or just add a link
to our webpage. Thank you :)
Regards,
Mikael LOAEC
Systems and Networks Administrator
URGI INRA
On 09/03/2016 18:47, Dan Bedard wrote:
> The iRODS dev team is certainly interested in how people are using and
want to use iRODS with Galaxy. Mikael, we would be happy to host the PDF
and/or a guest blog post about making it work. And we can provide some
assistance if there are difficulties on the iRODS side of this.
>
> Cheers,
> Dan Bedard
>
> —
> Dan Bedard
> Executive Director
> iRODS Consortium
>
> mobile: 1-919-346-3262
> email: danb(a)renci.org
> twitter: @DataDanB
>
> iRODS User Group Meeting 2016
> June 7-9 -- Chapel Hill, NC --
https://irods.org/ugm2016
>
>
>> Message: 2
>> Date: Wed, 9 Mar 2016 01:24:24 +0000
>> From: "Kandalaft, Iyad" <Iyad.Kandalaft(a)AGR.GC.CA>
>> To: James Taylor <james(a)bx.psu.edu>, Mohamed Kassam
>> <k.mamoud(a)gmail.com>
>> Cc: "galaxy-dev(a)lists.galaxyproject.org"
>> <galaxy-dev(a)lists.galaxyproject.org>
>> Subject: Re: [galaxy-dev] iRODS
>> Message-ID:
>> <CA1994D763C7444CB37EFC823D43C3824933F672(a)ONOTTAXES1.AGR.GC.CA>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> We were considering implementing data pull/push tools for Galaxy-iRODS
integration but we haven't started work on that.
>> I recall that the Galaxy team looked at backing Galaxy with iRODS but
moved away from the idea. There was a trello card with that information.
>>
>>
>> Iyad Kandalaft
>> Bioinformatics Systems Developer
>> Microbial Biodiversity Bioinformatics
>> Science & Technology Branch
>> Agriculture & Agri-Food Canada
>> Iyad.Kandalaft(a)agr.gc.ca | (613) 759-1228
>>
>> ________________________________________
>> From: galaxy-dev [galaxy-dev-bounces(a)lists.galaxyproject.org] on
behalf of James Taylor [james(a)bx.psu.edu]
>> Sent: March 8, 2016 10:09 AM
>> To: Mohamed Kassam
>> Cc: galaxy-dev(a)lists.galaxyproject.org
>> Subject: Re: [galaxy-dev] iRODS
>>
>> Mohamed,
>>
>> We implemented but never deployed the iRODS object store, so I suspect
>> it has not been tested much. If anyone out there is using it please
>> let us know.
>>
>> On Mon, Mar 7, 2016 at 10:30 AM, Mohamed Kassam <k.mamoud(a)gmail.com>
wrote:
>>> Dear all,
>>> I would like to use our interlan iRODs to pull data.
>>> I searched and i find that there is an object store for that.
>>> How it works ? DO I need to configure something else ?
>>>
>>> Thanks in advance,
>>>
>>>
>>> Mohamed
>>>
>>> ___________________________________________________________
>>> 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:
>>>
https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>
http://galaxyproject.org/search/mailinglists/
>> ___________________________________________________________
>> 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:
>>
https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>
http://galaxyproject.org/search/mailinglists/
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Wed, 9 Mar 2016 12:01:38 +0100
>> From: Mikael Loaec <mikael.loaec(a)versailles.inra.fr>
>> To: galaxy-dev(a)lists.galaxyproject.org
>> Cc: Olivier Inizan <Olivier.Inizan(a)versailles.inra.fr>
>> Subject: [galaxy-dev] iRODS
>> Message-ID: <56E00292.5070604(a)versailles.inra.fr>
>> Content-Type: text/plain; charset=utf-8
>>
>> Hi,
>>
>> @URGI, we have sucessfully tested connexion of galaxy instance with an
>> iRODS.
>> We have a pdf doc 67ko) explaining how we implement it if you want, but
>> don't know if i can send attachement on this mailinglist ?
>>
>> We (URGI) are also very interresting in data pull/push tools for
>> Galaxy-iRODS integration. Let us know when you will begin working on it.
>>
>> Regards,
>>
>> Mikael LOAEC
>> Systems and Networks Administrator
>> URGI INRA
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Wed, 9 Mar 2016 12:43:36 +0100
>> From: Mohamed Kassam <k.mamoud(a)gmail.com>
>> To: Mikael Loaec <mikael.loaec(a)versailles.inra.fr>
>> Cc: galaxy-dev(a)lists.galaxyproject.org, Olivier Inizan
>> <Olivier.Inizan(a)versailles.inra.fr>
>> Subject: Re: [galaxy-dev] iRODS
>> Message-ID:
>> <CAJrYSO8e2dfb2JjdAqCB9CFkg=
NELV8vrBCrwnQQ-FpKjU6Pkw(a)mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Thank you for your message,
>>
>> I sent to you Mikael an email if you can semd your pdf.
>>
>> It is a good idea to see if in The galaxy dev team they can integrate
iRODS
>> for the next release.
>>
>> Best regards,
>>
>> Mohamed
>>
>> 2016-03-09 12:01 GMT+01:00 Mikael Loaec <
mikael.loaec(a)versailles.inra.fr>:
>>
>>> Hi,
>>>
>>> @URGI, we have sucessfully tested connexion of galaxy instance with an
>>> iRODS.
>>> We have a pdf doc 67ko) explaining how we implement it if you want, but
>>> don't know if i can send attachement on this mailinglist ?
>>>
>>> We (URGI) are also very interresting in data pull/push tools for
>>> Galaxy-iRODS integration. Let us know when you will begin working on
it.
>>>
>>> Regards,
>>>
>>> Mikael LOAEC
>>> Systems and Networks Administrator
>>> URGI INRA
>>> ___________________________________________________________
>>> 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:
>>>
https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>
http://galaxyproject.org/search/mailinglists/
>>