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.lo...@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: d...@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.kandal...@agr.gc.ca>
> >> To: James Taylor <ja...@bx.psu.edu>, Mohamed Kassam
> >>      <k.mam...@gmail.com>
> >> Cc: "galaxy-dev@lists.galaxyproject.org"
> >>      <galaxy-dev@lists.galaxyproject.org>
> >> Subject: Re: [galaxy-dev] iRODS
> >> Message-ID:
> >>      <ca1994d763c7444cb37efc823d43c3824933f...@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.kandal...@agr.gc.ca | (613) 759-1228
> >>
> >> ________________________________________
> >> From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on
> behalf of James Taylor [ja...@bx.psu.edu]
> >> Sent: March 8, 2016 10:09 AM
> >> To: Mohamed Kassam
> >> Cc: galaxy-dev@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.mam...@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.lo...@versailles.inra.fr>
> >> To: galaxy-dev@lists.galaxyproject.org
> >> Cc: Olivier Inizan <olivier.ini...@versailles.inra.fr>
> >> Subject: [galaxy-dev] iRODS
> >> Message-ID: <56e00292.5070...@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.mam...@gmail.com>
> >> To: Mikael Loaec <mikael.lo...@versailles.inra.fr>
> >> Cc: galaxy-dev@lists.galaxyproject.org, Olivier Inizan
> >>      <olivier.ini...@versailles.inra.fr>
> >> Subject: Re: [galaxy-dev] iRODS
> >> Message-ID:
> >>      <CAJrYSO8e2dfb2JjdAqCB9CFkg=
> nelv8vrbcrwnqq-fpkju6...@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.lo...@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/
> >> -------------- next part --------------
> >
> >
> >
> >
> >
> >
> >
> > ___________________________________________________________
> > 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/
>
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