Hi, I (re-)installed galaxy on our server and managed to set it up to run jobs through our cluster (GridEngine). It's also running behind an Apache proxy now. But now I'm wondering how to setup to have the cluster jobs run as the real cluster users. I found the documentation on this topic a little thin. We use NIS for managing users and passwords across the cluster. How do I connect that to Galaxy? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
Hi Andreas: As far as I know Galaxy is designed to manage its own users and not to be integrated in any other platform. I think that the idea is to use galaxy as another user of your system. On 20/03/12 16:31, Andreas Kuntzagk wrote:
Hi,
I (re-)installed galaxy on our server and managed to set it up to run jobs through our cluster (GridEngine). It's also running behind an Apache proxy now. But now I'm wondering how to setup to have the cluster jobs run as the real cluster users. I found the documentation on this topic a little thin. We use NIS for managing users and passwords across the cluster. How do I connect that to Galaxy?
regards, Andreas
-- ===================================== Alfonso Núñez Salgado Unidad de Bioinformática Centro de Biologia Molecular Severo Ochoa C/Nicolás Cabrera 1 Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid (Spain) Phone: (34) 91-196-4633 Fax: (34) 91-196-4420 web: http://ub.cbm.uam.es/ =====================================
On Mar 22, 2012, at 12:30 PM, Alfonso Núñez Salgado wrote:
Hi Andreas:
As far as I know Galaxy is designed to manage its own users and not to be integrated in any other platform. I think that the idea is to use galaxy as another user of your system.
Hi Alfonso, Andreas is referring to recent changes that allow jobs to run as users other than the single Galaxy user that started the server process. See: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_a...
On 20/03/12 16:31, Andreas Kuntzagk wrote:
Hi,
I (re-)installed galaxy on our server and managed to set it up to run jobs through our cluster (GridEngine). It's also running behind an Apache proxy now. But now I'm wondering how to setup to have the cluster jobs run as the real cluster users. I found the documentation on this topic a little thin. We use NIS for managing users and passwords across the cluster. How do I connect that to Galaxy?
regards, Andreas
Andreas, You'll need to have Apache authenticate your users, as explained here: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy For NIS without Kerberos, you'd probably need to use mod_auth_pam to authenticate through your system's PAM stack. --nate
-- ===================================== Alfonso Núñez Salgado Unidad de Bioinformática Centro de Biologia Molecular Severo Ochoa C/Nicolás Cabrera 1 Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid (Spain) Phone: (34) 91-196-4633 Fax: (34) 91-196-4420 web: http://ub.cbm.uam.es/ =====================================
___________________________________________________________ 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:
Hi, On 26.03.2012 17:14, Nate Coraor wrote:
On Mar 22, 2012, at 12:30 PM, Alfonso Núñez Salgado wrote:
Hi Andreas:
As far as I know Galaxy is designed to manage its own users and not to be integrated in any other platform. I think that the idea is to use galaxy as another user of your system.
Hi Alfonso,
Andreas is referring to recent changes that allow jobs to run as users other than the single Galaxy user that started the server process. See:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_a...
Yes, that's what I wanted.
On 20/03/12 16:31, Andreas Kuntzagk wrote:
Hi,
I (re-)installed galaxy on our server and managed to set it up to run jobs through our cluster (GridEngine). It's also running behind an Apache proxy now. But now I'm wondering how to setup to have the cluster jobs run as the real cluster users. I found the documentation on this topic a little thin. We use NIS for managing users and passwords across the cluster. How do I connect that to Galaxy?
regards, Andreas
Andreas,
You'll need to have Apache authenticate your users, as explained here:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
For NIS without Kerberos, you'd probably need to use mod_auth_pam to authenticate through your system's PAM stack.
Thanks, I will look into it. regards, Andreas
--nate
-- ===================================== Alfonso Núñez Salgado Unidad de Bioinformática Centro de Biologia Molecular Severo Ochoa C/Nicolás Cabrera 1 Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid (Spain) Phone: (34) 91-196-4633 Fax: (34) 91-196-4420 web: http://ub.cbm.uam.es/ =====================================
___________________________________________________________ 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:
___________________________________________________________ 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:
-- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
Hi, after thinking more about this and also trying to get Apache use NIS (I failed with that :-( ) I just came up with an idea for a different solution: I don't use NIS for login into galaxy but when starting jobs I consult a mapping file (or the database) to map email addresses to know users. For unknown users I just continue to use the "galaxy" user. I guess a good starting point would be DRMAAJobRunner.queue_job Do you see any bigger problems coming my way? How best do I avoid to degress from the main tree to much? regards, Andreas On 27.03.2012 09:57, Andreas Kuntzagk wrote:
Hi,
On 26.03.2012 17:14, Nate Coraor wrote:
On Mar 22, 2012, at 12:30 PM, Alfonso Núñez Salgado wrote:
Hi Andreas:
As far as I know Galaxy is designed to manage its own users and not to be integrated in any other platform. I think that the idea is to use galaxy as another user of your system.
Hi Alfonso,
Andreas is referring to recent changes that allow jobs to run as users other than the single Galaxy user that started the server process. See:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_a...
Yes, that's what I wanted.
On 20/03/12 16:31, Andreas Kuntzagk wrote:
Hi,
I (re-)installed galaxy on our server and managed to set it up to run jobs through our cluster (GridEngine). It's also running behind an Apache proxy now. But now I'm wondering how to setup to have the cluster jobs run as the real cluster users. I found the documentation on this topic a little thin. We use NIS for managing users and passwords across the cluster. How do I connect that to Galaxy?
regards, Andreas
Andreas,
You'll need to have Apache authenticate your users, as explained here:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
For NIS without Kerberos, you'd probably need to use mod_auth_pam to authenticate through your system's PAM stack.
Thanks, I will look into it.
regards, Andreas
--nate
-- ===================================== Alfonso Núñez Salgado Unidad de Bioinformática Centro de Biologia Molecular Severo Ochoa C/Nicolás Cabrera 1 Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid (Spain) Phone: (34) 91-196-4633 Fax: (34) 91-196-4420 web: http://ub.cbm.uam.es/ =====================================
___________________________________________________________ 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:
___________________________________________________________ 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:
-- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
Hi, Ok, I was digging around for this and it seems to be a bit more involved then I expected. Problem is I don't really understand the interplay of DRMAAJobRunner and the user management. Can somebody provide me with some pointers? regards, Andreas On 28.03.2012 13:30, Andreas Kuntzagk wrote:
Hi,
after thinking more about this and also trying to get Apache use NIS (I failed with that :-( ) I just came up with an idea for a different solution:
I don't use NIS for login into galaxy but when starting jobs I consult a mapping file (or the database) to map email addresses to know users. For unknown users I just continue to use the "galaxy" user. I guess a good starting point would be DRMAAJobRunner.queue_job
Do you see any bigger problems coming my way? How best do I avoid to degress from the main tree to much?
regards, Andreas
On 27.03.2012 09:57, Andreas Kuntzagk wrote:
Hi,
On 26.03.2012 17:14, Nate Coraor wrote:
On Mar 22, 2012, at 12:30 PM, Alfonso Núñez Salgado wrote:
Hi Andreas:
As far as I know Galaxy is designed to manage its own users and not to be integrated in any other platform. I think that the idea is to use galaxy as another user of your system.
Hi Alfonso,
Andreas is referring to recent changes that allow jobs to run as users other than the single Galaxy user that started the server process. See:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_a...
Yes, that's what I wanted.
On 20/03/12 16:31, Andreas Kuntzagk wrote:
Hi,
I (re-)installed galaxy on our server and managed to set it up to run jobs through our cluster (GridEngine). It's also running behind an Apache proxy now. But now I'm wondering how to setup to have the cluster jobs run as the real cluster users. I found the documentation on this topic a little thin. We use NIS for managing users and passwords across the cluster. How do I connect that to Galaxy?
regards, Andreas
Andreas,
You'll need to have Apache authenticate your users, as explained here:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
For NIS without Kerberos, you'd probably need to use mod_auth_pam to authenticate through your system's PAM stack.
Thanks, I will look into it.
regards, Andreas
--nate
-- ===================================== Alfonso Núñez Salgado Unidad de Bioinformática Centro de Biologia Molecular Severo Ochoa C/Nicolás Cabrera 1 Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid (Spain) Phone: (34) 91-196-4633 Fax: (34) 91-196-4420 web: http://ub.cbm.uam.es/ =====================================
___________________________________________________________ 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:
___________________________________________________________ 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:
-- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
Hmm, I start feeling like I'm only talking to myself here :-) I finally have a prototyp running. Currently the mapping galaxy username <-> cluster username is only done using a dictionary in dmraa.py and should (and will) be moved to a configuration file. (Even better would be to put that into the database and should be editable by the admins but I'm afraid that is to much work for me right now.) I've added the diff and would appreciate if some expert would have a look on it and point out any glaring mistakes. There was a lot of guesswork about the inner workings of galaxy involved so I'm sure there are some bugs. regards, Andreas On 29.03.2012 16:12, Andreas Kuntzagk wrote:
Hi,
Ok, I was digging around for this and it seems to be a bit more involved then I expected. Problem is I don't really understand the interplay of DRMAAJobRunner and the user management. Can somebody provide me with some pointers?
regards, Andreas
On 28.03.2012 13:30, Andreas Kuntzagk wrote:
Hi,
after thinking more about this and also trying to get Apache use NIS (I failed with that :-( ) I just came up with an idea for a different solution:
I don't use NIS for login into galaxy but when starting jobs I consult a mapping file (or the database) to map email addresses to know users. For unknown users I just continue to use the "galaxy" user. I guess a good starting point would be DRMAAJobRunner.queue_job
Do you see any bigger problems coming my way? How best do I avoid to degress from the main tree to much?
regards, Andreas file:///home/kuntzagk/galaxy_diff
On 27.03.2012 09:57, Andreas Kuntzagk wrote:
Hi,
On 26.03.2012 17:14, Nate Coraor wrote:
On Mar 22, 2012, at 12:30 PM, Alfonso Núñez Salgado wrote:
Hi Andreas:
As far as I know Galaxy is designed to manage its own users and not to be integrated in any other platform. I think that the idea is to use galaxy as another user of your system.
Hi Alfonso,
Andreas is referring to recent changes that allow jobs to run as users other than the single Galaxy user that started the server process. See:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_a...
Yes, that's what I wanted.
On 20/03/12 16:31, Andreas Kuntzagk wrote:
Hi,
I (re-)installed galaxy on our server and managed to set it up to run jobs through our cluster (GridEngine). It's also running behind an Apache proxy now. But now I'm wondering how to setup to have the cluster jobs run as the real cluster users. I found the documentation on this topic a little thin. We use NIS for managing users and passwords across the cluster. How do I connect that to Galaxy?
regards, Andreas
Andreas,
You'll need to have Apache authenticate your users, as explained here:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
For NIS without Kerberos, you'd probably need to use mod_auth_pam to authenticate through your system's PAM stack.
Thanks, I will look into it.
regards, Andreas
--nate
-- ===================================== Alfonso Núñez Salgado Unidad de Bioinformática Centro de Biologia Molecular Severo Ochoa C/Nicolás Cabrera 1 Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid (Spain) Phone: (34) 91-196-4633 Fax: (34) 91-196-4420 web: http://ub.cbm.uam.es/ =====================================
___________________________________________________________ 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:
___________________________________________________________ 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:
-- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
participants (3)
-
Alfonso Núñez Salgado -
Andreas Kuntzagk -
Nate Coraor