Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Hi, all, We are in the process of setting up Galaxy as a big university framework for the entire university and world-wide free academic access. We currently have a portal (www.bioportal.uio.no) which is bioinformatics oriented. The Galaxy we are setting up will give access to more than 100 applications and will include the following features: - Apache proxy enabled - implemented - PostgreSQL located in another host - - implemented - sending jobs to a cluster (using SLURM, drmaa) - implemented - identification via SAML2 - (not OpenID) - implementaiton phase now, problems with reading the response from IdP If any of you has experience in pysaml2 + WSGI, please let me know. In turn, I am willing to share our experience so far with the issues above. Best regards Nikolay On Sun, 29 Apr 2012 17:11:05 +1200, Edward Hills ehills...@gmail.com wrote: 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/ -- Nikolay Vazov, PhD Research Computing Centre - http://hpc.uio.no USIT, University of Oslo ___ 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 Ryan, I like that it's user-directed, and we could be there to provide input, although if help is needed to organize the call we could probably assist with that. I plan to be on the call as often as my schedule allows, and I believe some of the other developers on the team would also be interested. --nate On Apr 28, 2012, at 8:49 AM, Ryan Golhar wrote: One question - Are the Galaxy developers involved in this or is this for user's only? It may be helpful to have developers on the call to provide information that users do not necessarily have. On Fri, Apr 27, 2012 at 8:21 PM, steve.mcma...@csiro.au wrote: Sounds like a good idea to me. I'm sure the time will be awkward due to the time zone difference. I'm at UTC+10. Regards. Steve McMahon Solutions architect senior systems administrator ASC Cluster Services Information Management Technology (IMT) CSIRO Phone: +61-2-62142968 | Mobile: +61-4-00779318 steve.mcma...@csiro.au | www.csiro.au PO Box 225, DICKSON ACT 2602 1 Wilf Crane Crescent, Yarralumla ACT 2600 -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Ann Black-Ziegelbein Sent: Saturday, 28 April 2012 4:45 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally? 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/ ___ 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/ ___ 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/ ___ 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?
We've also started a local deployment for University of Illinois Urbana-Champaign. So I would be interested in participating. Chris On Apr 27, 2012, at 2:32 PM, David Hoover hoove...@helix.nih.gov wrote: Not a bad idea. Most of the conversations on this list are very limited and detailed in scope, dealing with the minutia of tools and variables. There isn't much on the bird's eye view. I'm in. On Apr 27, 2012, at 2:45 PM, Ann Black-Ziegelbein wrote: 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/ ___ 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/ ___ 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] Unable to set BAM Metadata
This is my code for running a samtools command internally, via Galaxy: open INP, $ARGV[0] or die Cannot open file: $!; $file = $ARGV[1]; open OUT, $file or die Cannot open file: $!; @out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] 21`; print OUT @out; close INP; close OUT; The 21 is used to redirect the STDERR to STDOUT. When I run this in the console, it gives a non-empty file. But when run it in Galaxy, Galaxy can no longer find the path. This error message is given to me. Traceback (most recent call last): File /home/applications/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 126, in run_job job_wrapper.finish( stdout, stderr ) File /home/applications/galaxy-dist/lib/galaxy/jobs/__init__.py, line 618, in finish dataset.set_meta( overwrite = False ) File /home/applications/galaxy-dist/lib/galaxy/model/__init__.py, line 874, in set_meta return self.datatype.set_meta( self, **kwd ) File /home/applications/galaxy-dist/lib/galaxy/datatypes/binary.py, line 179, in set_meta raise Exception, Error Setting BAM Metadata: %s % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found The weird thing is, when I remove the 21 from the code and run it again in Galaxy, I am able to get this diagnostic message: [samopen] SAM header is present: 66338 sequences. This is the reason why I added the 21 in the first place, so that this diagnostic message would be 'ignored' (since it is detected as an error). Now, if the other code (the one without 21) is able to produce the aforementioned diagnostic message, then I assume that it is able to at least execute the samtools command internally. But when I add the 21, galaxy can no longer find the command. Do I need to specify a path somewhere in the galaxy-dist? I apologize for the very long message. Thanks in advance, CL ___ 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] What does this line of code mean
Hi all, Can I ask what this line of code does? job_wrapper.finish( stdout, stderr ) It's the one from the local.py. Cheers, CL ___ 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
Hi Ann I am running an instance at The University of Sydney GMT+10 and would like to be part of any such online talk. Regards, Matloob ___ 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 Ryan, Ann, and everyone else I second what Nate says (I always do :-). I too like that it is user driven. And, while I am not a developer, I do plan on being on the call as often as possible. I can also offer my support for logistical and any other support. Ann, please let me know if you want help with getting this going and getting the word out. On a related note, With Matloob's email, we have at least 3 organizations in Australia and New Zealand that are interested. I know that there are many more Galaxy installations in that part of the world (and you have Enis and Ross in Australia now). Would this be a good opportunity to set up the first (to my knowledge) regional user group? If anyone thinks this is a good idea, please respond (and create a new thread). Finally, Ann, thanks for starting this. Dave C I also that both Ross and Enis are in Australia now On Sun, Apr 29, 2012 at 10:24 AM, Nate Coraor n...@bx.psu.edu wrote: Hi Ryan, I like that it's user-directed, and we could be there to provide input, although if help is needed to organize the call we could probably assist with that. I plan to be on the call as often as my schedule allows, and I believe some of the other developers on the team would also be interested. --nate On Apr 28, 2012, at 8:49 AM, Ryan Golhar wrote: One question - Are the Galaxy developers involved in this or is this for user's only? It may be helpful to have developers on the call to provide information that users do not necessarily have. -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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?
To all interested in Dave's suggestion: IMHO, an Australian/New Zealand Galaxy user/deployer/developer group will be worth setting up and will be viable if it solves specific problems that aren't adequately addressed by existing networks and communication channels - otherwise it will be JAFUG (just another fleeting user group) and will likely fizzle due to lack of genuine utility to potential participants. EG: One challenge for us when it comes to (eg) the proposed teleconferences is the tyranny of time zones - being 14 hours ahead of EST eg in Melbourne/Sydney. The other big challenge is that travel to meetings in Europe or the USA is expensive and exhausting, so workshops and hands on training are harder to get to. In general, I think we're probably going to be able to find plenty of problems to do with geographic isolation and maybe even some specific Australian challenges - but let's be clear about exactly what those are before we start building any structures. One problem I keep seeing is that there are many organisations happy to invest in hardware infrastructure, but far less willing to invest in the training and staff development needed for success. Two things I'd like to suggest to help with planning: 1) to get a better idea of scope, it would be very handy to assemble a register of potential organisations and their primary contacts. I already know of some large Australian organisations investing heavily in Galaxy deployment - eg - VLSCI in Melbourne; UQ in Brisbane, CSIRO all over the place, the Victorian DPI, AGRF, and the BakerIDI where I'm based - no doubt there are plenty of others too? 2) to make sure the idea is viable, it would be useful to collect some specific deployment challenges that people are experiencing that some kind of local user's group could help overcome? One focus I have a personal interest in exploring would be in face to face educational activities: eg for local Galaxy instance system administrators? Local tool developers? Local biologist users in specific contexts like short read sequencing? Suggestions welcomed... On Mon, Apr 30, 2012 at 12:37 PM, Dave Clements cleme...@galaxyproject.org wrote: Hi Ryan, Ann, and everyone else I second what Nate says (I always do :-). I too like that it is user driven. And, while I am not a developer, I do plan on being on the call as often as possible. I can also offer my support for logistical and any other support. Ann, please let me know if you want help with getting this going and getting the word out. On a related note, With Matloob's email, we have at least 3 organizations in Australia and New Zealand that are interested. I know that there are many more Galaxy installations in that part of the world (and you have Enis and Ross in Australia now). Would this be a good opportunity to set up the first (to my knowledge) regional user group? If anyone thinks this is a good idea, please respond (and create a new thread). Finally, Ann, thanks for starting this. Dave C I also that both Ross and Enis are in Australia now On Sun, Apr 29, 2012 at 10:24 AM, Nate Coraor n...@bx.psu.edu wrote: Hi Ryan, I like that it's user-directed, and we could be there to provide input, although if help is needed to organize the call we could probably assist with that. I plan to be on the call as often as my schedule allows, and I believe some of the other developers on the team would also be interested. --nate On Apr 28, 2012, at 8:49 AM, Ryan Golhar wrote: One question - Are the Galaxy developers involved in this or is this for user's only? It may be helpful to have developers on the call to provide information that users do not necessarily have. ___ 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/
