[galaxy-dev] galaxy.ini
Hi For the woefully inept, where in the heck is galaxy.ini stored? I saw the documentation that said change 127.0.0.1 to 0.0.0.0 and the file name, can't find it to do so. I know it all works as I've installed a module and that all shows up and works on localhost. Thanks Bryan ___ 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/
Re: [galaxy-dev] User is not allowed to view history
She got that error message when she clicked on settings and tried to view saved histories. It looks like this error when loading '/history/view' was fixed with release_13.02: https://github.com/galaxyproject/galaxy/commit/3deac8edfba8e8088de855789a28e7d3a328b9b5 If possible, you could update to git branch release_13.02 and get the fix. Alternately, you could apply that particular patch above to your current installation but that may cause more conflicts later if you decide to update. saw that their history wasn't loading on the right-hand side. The above does not help the underlying problem of the user's history erroring in the 'Analyze Data' page. If you or the user open the javascript console: http://webmasters.stackexchange.com/questions/8525/how-to-open-the-javascript-console-in-different-browsers and attempt to load the history, do you see any javascript errors? Do you see any errors in the server log when he/she attempts to load the history? On Mon, Jul 13, 2015 at 11:38 AM, Lina L Faller lina.fal...@gmail.com wrote: Hi Carl, Thanks for getting back to me! - The galaxy version is release_2013.01.13. - The user logged into their galaxy account and saw that their history wasn't loading on the right-hand side. She got that error message when she clicked on settings and tried to view saved histories. - It's not an imported history, she has had the same history since she first logged in. Thanks for any advice you might have! Cheers, ~Lina On Mon, Jul 13, 2015 at 11:24 AM, Carl Eberhard carlfeberh...@gmail.com wrote: Hi, Lina Apologies for the delay. A few questions, please: - What version is your Galaxy instance running? - What URL or operation is the user trying when they get that error? Is it just the 'Analyze Data' page or something else like 'galaxy/history/view?id=id'? - Is the history imported? Is it accidentally/possibly from a different user/account? On Tue, Jul 7, 2015 at 3:19 PM, Lina L Faller lina.fal...@gmail.com wrote: Hi all, I am new to maintaining the galaxy server at my institute and a user emailed me that they get the following error message when trying to view their history: Either you are not allowed to view this history or the owner of this history has not made it accessible. Is there a way to modify access privileges of the users' histories? Thanks for any advice! ~Lina ___ 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/
Re: [galaxy-dev] galaxy.ini
It is under config/. You’ll want to copy it from /config/galaxy.ini.sample Thanks for using Galaxy, Dan On Jul 14, 2015, at 6:35 AM, Bryan Hepworth bryan.hepwo...@newcastle.ac.uk wrote: Hi For the woefully inept, where in the heck is galaxy.ini stored? I saw the documentation that said change 127.0.0.1 to 0.0.0.0 and the file name, can't find it to do so. I know it all works as I've installed a module and that all shows up and works on localhost. Thanks Bryan ___ 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/
Re: [galaxy-dev] galaxy.ini
Hi Bryan, if you are running a old Galaxy instance this file was called universe_wsgi.ini and was located in your Galaxy root folder. Cheers, Bjoern On 14.07.2015 12:35, Bryan Hepworth wrote: Hi For the woefully inept, where in the heck is galaxy.ini stored? I saw the documentation that said change 127.0.0.1 to 0.0.0.0 and the file name, can't find it to do so. I know it all works as I've installed a module and that all shows up and works on localhost. Thanks Bryan ___ 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/
Re: [galaxy-dev] Galaxy server build
We run the galaxy server as a vm… for 0-30 simultaneous users on a similar size cluster. 16 virtual cores and 8G RAM. I use 4 web handlers and 2 job handlers behind nginx. Brad On Jul 14, 2015, at 1:13 PM, Benjamin Datko bda...@carc.unm.edumailto:bda...@carc.unm.edu wrote: Hello All, We am attempting to build a local galxay server and we are looking for some advice. The plan is to purchase a decdicated server to host galaxy and communicate with our IBM System x3755 120 node computer cluster running TORQUE/Maui resource manger and scheduler. Do you have an recomendations on the configuration and adequate hardware for the server. The server will only act as a gateway to users, but will not do any computational heavy lifting. If anyone has had experience with this kind of setup, could you offer any further suggestions? -Ben ___ 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/
[galaxy-dev] Workflow editor stuck on loading workflow
It looks like a recent commit since 6/26 to 15.05 is break the workflow editor. I have a pipeline I'm trying to edit. I updated my instance of Galaxy and now when I try to edit a workflow, the editor is stuck at Loading workflow editor. ___ 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/
[galaxy-dev] Nob able to upload even 25MB of file for running metaphlan on public Galaxy sever.
Hi, I am trying to run metaphlan on the Galaxy public website, but even a 25MB file cannot be uploaded for analysis. It says the size is too large. And to run metaphlan on local it is just a nightmare because there is absolutely no tutorial of how to install all the prerequisites for material and metaphlan itself. Please see if you can extend the upload file size to atleast 1GB on the galaxy public server of size or atleast have a tutorial for running metaphlan locally. ___ 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/
Re: [galaxy-dev] cloudman galaxy - too large volume
I just fixed this here https://github.com/galaxyproject/cloudman/commit/0f6ab132958ad57a338c66387112407edbc7632d#diff-9eba488c9175de87945a13d7b7228a6dR621 This required switching to SSD-based volumes on AWS and, besides actually being able to create volumes up to 16TB now, it should give us better IO performance now. On Mon, Jul 13, 2015 at 5:06 PM, Alexander Vowinkel vowinkel.alexan...@gmail.com wrote: Hi, I get this error on cluster creation: Error creating volume: EC2ResponseError: 400 Bad Request InvalidParameterValueVolume of 2048GiB is too large for volume type standard; maximum is 1024GiB Is there a way to get a volume that big for galaxy? Best, Alexander ___ 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/
