Re: [galaxy-dev] Impersonate a User
Hi Greg, Try clicking the logout button. That should logout of the user you are impersonating and back into you. Although, this does have a few quirks also and may log you right out. Don't forget that when you are impersonating someone the history may not be automatically loaded and you will have to do that manually. Cheers, Ed ___ 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] xgrid cluster computing
Hi Galaxy team, So our university has decided to switch our xgrid clusters back on and we are looking to set Galaxy up on these. Has anyone got (or tried) to set up Galaxy on xgrid before? xgrid supposedly conforms to DRMAA so technically Galaxy should work, correct? Cheers, Ed ___ 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] Parallelism tag and job splitter
Hi Peter, thanks again. Turns out that it has been implemented by the looks of it in lib/galaxy/datatypes/tabular.py under class Vcf. However, despite this, it is always the Text class in data.py that is loaded and not the proper Vcf one. Can you point me in the direction of where the type is chosen? Cheers, Ed On Wed, Oct 31, 2012 at 9:46 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wednesday, October 31, 2012, Edward Hills wrote: Thanks Peter. My next question is, I have found that VCF files don't get split properly as the header is not included in the second file as is usually required by tools (such as vcf-subset). I have read the code and am happy to implement this functionality but am not to sure where this would best be done. I see a class Text ( data ) which looks like every datatype is sent to. Would it be best to implement a VCF class which is called when the datatype is VCF? Cheers, Ed VCF is I assume defined as a subclass of Text, so inherits the naive simple splitting implemented for text files (which doesn't know about headers). Have a look at the SAM splitting code (under lib/galaxy/datatypes/*.py) as an example where header aware splitting was done. You'll probably need to implement something similar. Peter ___ 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] Parallelism tag and job splitter
Hi Galaxy-Team, After reading a message on this mailing list about the job splitter I began to investigate what and how this is used. Unfortunately I have been unable to find any documentation on your website for it. Am I blind and missing it or is it yet to be properly documented? Sorry if this turns to be out a pointless exercise, but it would be extremely useful for my Galaxy development. Cheers, Ed ___ 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] Parallelism tag and job splitter
Thanks Peter. My next question is, I have found that VCF files don't get split properly as the header is not included in the second file as is usually required by tools (such as vcf-subset). I have read the code and am happy to implement this functionality but am not to sure where this would best be done. I see a class Text ( data ) which looks like every datatype is sent to. Would it be best to implement a VCF class which is called when the datatype is VCF? Cheers, Ed On Wed, Oct 31, 2012 at 12:35 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Tue, Oct 30, 2012 at 11:20 PM, Edward Hills ehills...@gmail.com wrote: Hi Galaxy-Team, After reading a message on this mailing list about the job splitter I began to investigate what and how this is used. Unfortunately I have been unable to find any documentation on your website for it. Am I blind and missing it or is it yet to be properly documented? Sorry if this turns to be out a pointless exercise, but it would be extremely useful for my Galaxy development. Cheers, Ed Hi Ed, To enable this you need to add a parallelism tag to the tool's XML file, and enable the feature in universe_wsgi.ini with something like this: use_tasked_jobs = True local_task_queue_workers = 4 I'm not aware of any documentation, I've been mostly working from the Python source code in order to get it to work on the BLAST+ wrappers and some of my other tool wrappers. In all the cases I've used there is a single FASTA file being split, sometimes some common input files which are unchanged, and a single output file being merged. Peter ___ 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] Workflow Queue
Hi Galaxy team, I am wanting to know where to find the queue that stores all tool's that are going to be executed in the pipeline. For example, I am running a workflow of 5 tools all linked together (the details are not important). Programatically I wish to know the names of the tools that are going to be run. This is because I wish to perform some pre-run analysis on all the tools in the workflow before they get executed. Thanks, Edward Hills Department of Biochemistry, University of Otago, Dunedin, New Zealand. ___ 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] Refreshing side bar
Hi Guys, So i'm looking at having the dataset history item that is currently running to load in text from a txt file, re-reading the txt file every few seconds or so. I have found where it gets displayed in the /templates/root/history_common.mako and have added %include file=test.txt/ so that it will read my text file but that obviously just reads it the once and then moves on. So what I need help with is being able to read it from the file multiple times while the tool is executing. Any help would be greatly appreciated. Cheers, Ed Department of Biochemistry, University of Otago, Dunedin, New Zealand. ___ 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] Jobs waiting in job queue
Hi Galaxy team, This is going to be a very unhelpful message but I hope you have some ideas to point me in the right direction! For some reason our local Galaxy instance (set up with the production server guide on the wiki minus all the fancy cluster stuff) is refusing to run jobs except after a restart. So we wish to execute our particular tool, it shows up in the history as grey and will remain that way. I have investigated all the logs and there are no error messages and for some reason the handler is not receiving the message to execute the tool. Once we reset Galaxy as soon as it has gone through its initial start-up process it executes our tool we wanted it to with no problems. We are operating with the latest version of galaxy-dist as of 30/07/12. I have investigated the web and manager logs as well as my apache logs just in case and have come up short. Any tips or ideas would be much appreciated! Cheers, Ed Department of Biochemistry, University of Otago, Dunedin, New Zealand. ___ 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] Interested in speaking with other institutions deploying Galaxy locally?
RE: The chat about NZ/AUS communication us here at Otago University (Dunedin, NZ) are very very keen for this. Please email us at edward.hi...@otago.ac.nz if this does decide to take off :) Cheers, Ed ___ 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] Interested in speaking with other institutions deploying Galaxy locally?
Hi Ann, We are in the process of doing the same thing here at the University of Otago (New Zealand). If we are able to sort something via the timezone difference (we are GMT+12, first to see the sun!) we would very much be interested. Cheers, Ed Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ 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] Looking where to edit web view
Hello Galaxy team, I've recently begun building a resource usage monitor / predictor for Galaxy as part of my Computer Science Honours degree and I was wanting to at some later stage in my project, once the actual resource monitor is built, to incorporate it to the actual Galaxy web interface. have been looking through your code and have found it somewhat difficult to track down where exactly i would go about doing this. I would like to ahve a separate tab up in the top nav bar and then be able to display resource information about Galaxy when its running (processes, I/O, RAM, CPU etc.) Are you able to point me in the right direction for this? Thankyou, Ed ___ 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/
