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@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@AGR.GC.CA> To: James Taylor <james@bx.psu.edu>, Mohamed Kassam <k.mamoud@gmail.com> Cc: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] iRODS Message-ID: <CA1994D763C7444CB37EFC823D43C3824933F672@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@agr.gc.ca | (613) 759-1228
________________________________________ From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of James Taylor [james@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.mamoud@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@versailles.inra.fr> To: galaxy-dev@lists.galaxyproject.org Cc: Olivier Inizan <Olivier.Inizan@versailles.inra.fr> Subject: [galaxy-dev] iRODS Message-ID: <56E00292.5070604@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@gmail.com> To: Mikael Loaec <mikael.loaec@versailles.inra.fr> Cc: galaxy-dev@lists.galaxyproject.org, Olivier Inizan <Olivier.Inizan@versailles.inra.fr> Subject: Re: [galaxy-dev] iRODS Message-ID: <CAJrYSO8e2dfb2JjdAqCB9CFkg=NELV8vrBCrwnQQ-FpKjU6Pkw@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@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 --------------
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@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@AGR.GC.CA> To: James Taylor <james@bx.psu.edu>, Mohamed Kassam <k.mamoud@gmail.com> Cc: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] iRODS Message-ID: <CA1994D763C7444CB37EFC823D43C3824933F672@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@agr.gc.ca | (613) 759-1228
________________________________________ From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of James Taylor [james@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.mamoud@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@versailles.inra.fr> To: galaxy-dev@lists.galaxyproject.org Cc: Olivier Inizan <Olivier.Inizan@versailles.inra.fr> Subject: [galaxy-dev] iRODS Message-ID: <56E00292.5070604@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@gmail.com> To: Mikael Loaec <mikael.loaec@versailles.inra.fr> Cc: galaxy-dev@lists.galaxyproject.org, Olivier Inizan <Olivier.Inizan@versailles.inra.fr> Subject: Re: [galaxy-dev] iRODS Message-ID: <CAJrYSO8e2dfb2JjdAqCB9CFkg=NELV8vrBCrwnQQ-FpKjU6Pkw@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@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/
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@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@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@AGR.GC.CA> To: James Taylor <james@bx.psu.edu>, Mohamed Kassam <k.mamoud@gmail.com> Cc: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] iRODS Message-ID: <CA1994D763C7444CB37EFC823D43C3824933F672@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@agr.gc.ca | (613) 759-1228
________________________________________ From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of James Taylor [james@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.mamoud@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@versailles.inra.fr> To: galaxy-dev@lists.galaxyproject.org Cc: Olivier Inizan <Olivier.Inizan@versailles.inra.fr> Subject: [galaxy-dev] iRODS Message-ID: <56E00292.5070604@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@gmail.com> To: Mikael Loaec <mikael.loaec@versailles.inra.fr> Cc: galaxy-dev@lists.galaxyproject.org, Olivier Inizan <Olivier.Inizan@versailles.inra.fr> Subject: Re: [galaxy-dev] iRODS Message-ID: <CAJrYSO8e2dfb2JjdAqCB9CFkg= NELV8vrBCrwnQQ-FpKjU6Pkw@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@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/
participants (3)
-
Dan Bedard -
Mikael Loaec -
Mohamed Kassam