[galaxy-dev] Reload a tool from the command line
Hello evyerbody, i guess this question has already been answered, but i didn't find any :/ Is there a way to reload a tool file from the command line ? I'd like to automate the process when a user upload a new version of an existing tool. Am I reinventing the wheel here, is there something already existing for this purpose ? Regards, Jean-Baptiste ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] change queue with sge
On 05/03/2011 03:11 PM, Sylvain Thomas wrote: > Hi > > I currently use a galaxy server with cluster. This cluster uses SGE. > I'd like to specify a queue other than the default. > I have tried many combinaisons with drmaa:/// without success. The queue > used is always the default one. Here is what i use : start_job_runners = drmaa default_cluster_job_runner = drmaa://-q galaxy -V/ Regards, Jean-Baptiste ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Multiple galaxy instances
Hello everybody, i'm in the process to provide Galaxy for multiple team. I've already setup a testing instance using the production setup page on the wiki (apache + sge) and it works quite well if i'm refearing to the users feedback. This setup is typically use for NGS dealing with data on a NFS share without uploading them to the instance. Why do i need multiple instance ? Maybe i'm not using galaxy correctly. Correct me if i'm wrong. My goal is to delagate the management of library/datasets to a galaxy admin of each team from the beginning : i do NOT want a SINGLE independant super admin to manage the access for multiple team, it doesn't scale. The galaxy instance and the underlying "galaxy" system user must access to the NGS data on the NFS (v3) share. This means that the galaxy user must be in a group that has access to the data. I can delegate the process of managing datasets and library to a dedicated galaxy admin. This setup is working quite well with the single instance setup. My job as a sysadmin is reduced to galaxy setup and maintenance : i'm not involved in the library/dataset management. The problem with this setup does not work if there is another team with data they don't want to share with others (don't blame me on that) : the galaxy system user must access the data of the first team AND the second team, this means that the galaxy admin of each team could access everything. One solution to this problem would be to have an independant galaxy super admin with access to everything which manage data access to each team. I don't like this solution, like i said, it doesn't scale. So, another way to deal with that is to give each team its own galaxy instance (each running with a specific system galaxy user) with a dedicated galaxy admin. Two possibility : - N galaxy tree, each with a different tuned universe_wsgi.ini init file (dedicated path, port, database, etc...). The problem here is on the sysadmin side : the update process effort must be repeated N times. - A unique galaxy tree, and N tuned (dedicated path, port, database, etc...) universe_wsgi.ini files. This seems the best to me but i need to know if galaxy internals can managed that kind of setup ? What do you think ? Any inputs, remarks or advices are welcome ! Regards, Jean-Baptiste ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Only use filepaths and "Copy data into Galaxy?"
On 02/25/2011 04:20 PM, Nate Coraor wrote: > Hi Jean-Baptiste, > > This is certainly a concern. It's not possible to do this without some > hackery, but it's minor hackery. If you're certain you'll never want to > have that box unchecked, you can make the following change to > templates/library/common/common.py: > - link_data_only_field = ' value="No"%s/>No' % checked > + link_data_only_field = ' value="No" checked disabled/>No' > Alternatively, you could add 'checked' but not 'disabled' to make it the > default but still modifiable. > > --nate Thank your for this very precise answer. I'd rather not change the source by myself, but i'll keep this tip in mind if i need to prevent file upload. jbd ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Only use filepaths and "Copy data into Galaxy?"
Hello everybody, i've got one galaxy server running. The ressource on the wiki are very useful for that purpose, thank you. I've got one question regarding data library when using "upload files from filesystem paths". There is a checkbox, unchecked by default, which prevent file upload into Galaxy. Is there a way to activate this checkbox by default, or to totally remove it on a per library basis ? I'm afraid of data libraries admin forgetting to check this box :D Regards, Jean-Baptiste ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Upload files from filesystem paths for non admin users
On 02/03/2011 07:35 PM, Greg Von Kuster wrote: > Hello Jean-Baptiste, > > Running the latest revision in the distribution, (4895:ad933d160a7c), > I have followed your steps precisely and do not see the behavior you state. Hello, thank you for having trying to reproduce my problem. I've updated my Galaxy installation, and the problem is gone. Sorry for the delay of my answer, but i just had the time to test it this morning. Regards, Jean-Baptiste ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Upload files from filesystem paths for non admin users
Hello everybody, i'm sorry for posting again. I didn't have any answer during the christmas holiday, so i take another (and last) chance :) I'm running a fresh galaxy-dist installation (changeset 4640:8729d2e29b02) on a Centos 5.5 distribution. I'm using LDAP authentication through Apache. Here is the situation. As a galaxy admin, i've created a "new data library" called "TP" through the admin interface. I've another user, called "foobar" which belongs to a group called "TP Admin" which is associated to the role "TP Admin". I've edited the permissions of the "TP" library to only associate "TP Admin" role to "add library item". No other entry is associated with any role. The "foobar" user logs into galaxy and go to "Shared Data/Data libraries". He chooses "TP" and click on "Add datasets". The problem is that the option "Upload files from filesystem paths" appears in the scrolling "upload option" list even if "foobar" is not a galaxy admin. This means that he can virtually access any file on the filesystem. The comments in the "universe_wsgi.ini" mention "Please note the security implication that this will give Galaxy Admins access to anything your Galaxy user has access to." which seems ok for Galaxy admins, but it looks like this is also the case for any galaxy user. Any advice on this behaviour? Maybe i misunderstood something. Regards, Jean-Baptiste Denis ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
[galaxy-dev] Upload files from filesystem paths for non admin users
Hello everybody, I'm running a fresh galaxy-dist installation (changeset 4640:8729d2e29b02) on a Centos 5.5 distribution. I'm using LDAP authentication through Apache. Here is the situation. As a galaxy admin, i've created a "new data library" called "TP" through the admin interface. I've another user, called "foobar" which belongs to a group called "TP Admin" which is associated to the role "TP Admin". I've edited the permissions of the "TP" library to only associate "TP Admin" role to "add library item". No other entry is associated with any role. The "foobar" user logs into galaxy and go to "Shared Data/Data libraries". He chooses "TP" and click on "Add datasets". The problem is that the option "Upload files from filesystem paths" appears in the scrolling "upload option" list even if "foobar" is not a galaxy admin. This means that he can virtually access any file on the filesystem. The comments in the "universe_wsgi.ini" mention "Please note the security implication that this will give Galaxy Admins access to anything your Galaxy user has access to." which seems ok for Galaxy admins, but it looks like this is also the case for any galaxy user. Any advice on this behaviour? Maybe i misunderstood something. Regards, Jean-Baptiste Denis ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
