Re: [galaxy-dev] 2011 Galaxy Community Conference, May 25-26, Lunteren, The Netherlands
Hello all, This is a reminder that early registration for the 2011 Galaxy Community Conference closes in less than two weeks. You can save 20% on registration if you register on or before 24 April. http://galaxy.psu.edu/gcc2011/Register.html We've also added a partial list of confirmed speakers. More will be added in the coming weeks as the schedule firms up. http://galaxy.psu.edu/gcc2011/Programme.html Please let me know if you have any questions, and hope to see you in May, Dave C. On Tue, Feb 1, 2011 at 9:19 PM, Dave Clements clementsgal...@gmail.comwrote: Hello all, We are pleased to announce the *2011 Galaxy Community Conference*, being held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your own and your community's research. *Link: http://galaxy.psu.edu/gcc2011/ * *Overview * This event aims to engage a broader community of developers, data producers, tool creators, and core facility and other research hub staff to become an active part of the Galaxy community. We'll cover defining resources in the Galaxy framework, increasing their visibility and making them easier to use and integrate with other resources, how to extend Galaxy to use custom data sources and custom tools, and best practices for using Galaxy in your organization. Additional topics include, but are not limited to: * Talks submitted by the Galaxy community * Integration of tools (including NGS analysis tools) and distributed job management * Deployment of Galaxy instances on local resources and on the Cloud * Management of large datasets with the Galaxy Library System * Using the Galaxy LIMS functionality at NGS sequencing facilities * Visualizing Data without leaving Galaxy * Performing reproducible research * Performing and sharing complex analyses with Workflows * An Introduction to Galaxy session, offered on May 24, for Galaxy newcomers. *Registration * The conference fee is €100 on or before April 24, and €120 after that. The meeting is being held at the Conference Centre De Werelt in Lunteren, The Netherlands, which is also the conference hotel. You are encouraged to register early, as space at the hotel (and at the Intro to Galaxy session) is limited and is likely to fill up before the conference itself does. *Link: http://galaxy.psu.edu/gcc2011/Register.html ** Abstract Submission * Abstracts are now being accepted for short oral presentations. Proposals on any topic of interest to the Galaxy community are welcome and encouraged. The abstract submission deadline is the end of February 28. *Link: http://galaxy.psu.edu/gcc2011/Abstracts.html * *Sponsors * The 2011 Galaxy Community Conference is co-sponsored by the US National Science Foundation (NSF), and the Netherlands Bioinformatics Centre (NBIC). NBIC is a collaborative institute of the bioinformatics groups in the Netherlands. Together, these groups perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. *Links: http://www.nbic.nl/ and http://www.nsf.gov/ * We are looking forward to a great conference and hope to see you in the Netherlands! The Galaxy and NBIC Teams -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ ___ 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] Recommended Specs for Production System
On Apr 8, 2011, at 11:01 AM, Dave Walton wrote: This is very close to our config, except - We run all of this on a 4 core Virtual Machine running SUSE Linux Enterprise Server 11 (x86_64) with 16 GB of memory. Instead of SGE our HPC cluster uses Torque/Moab for scheduling. Also, we've set up a separate IO Node for upload of data files from the file system and FTP (correct me if I mis-spoke Glen). Also, instead of apache we run nginx for our httpd server as it was easy to get off-loading of file upload and download working with that server. We're not seeing a heavy load from users at this point, but this has worked pretty well for us so far. Hope this helps, Dave The only reason we offload the upload jobs somewhere other than our HPC cluster is that our cluster nodes do not see the outside world. Our IT folks did not really want to change the network configuration, so we installed TORQUE on a spare Linux server, mounted our galaxy network storage on it, and we setup some upload specific job runners that send those jobs to that node. If you have NAT setup on your cluster you probably don't need to worry about that. We have pretty fat cluster nodes (128GB RAM and 32 cores) since we run a lot of multi-threaded jobs on the cluster but not a lot of MPI jobs. Our NGS tools are typically configured to use 16-32 threads. On 4/8/11 10:21 AM, Assaf Gordon gor...@cshl.edu wrote: Assaf Gordon wrote, On 04/08/2011 10:07 AM: Processes: The servers processes that you should plan for are: 1 galaxy process for job-runner 2 or 3 galaxy processes for web-fronts 1 process of postgres 1 process of apache optionally 1 process of galaxy-reports you'll also want to leave some free CPUs for SSH access, CRON jobs and other peripherals. Postgres apache are multithreaded, but it usually balances out with light load on the web/DB front from galaxy (even with 30 users). So all in all, I'd recommend reserving 5 to 8 CPU cores to just galaxy and daemons (reserving means: never using those cores for galaxy jobs). You can do with less cores, but then response times might suffer (and it's annoying when you click show saved histories and the page takes 20 seconds to load...). Forgot to mention SGE/PBS: you definitely want to use them (even if you're using a single machine), because the local job runner doesn't take into account multi-threaded programs when scheduling jobs. So another core is needed for the SGE scheduler daemons (sge_qmaster and sge_execd). ___ 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/ -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153 ___ 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] Question about cuffcompare tool implementation
Assaf, Assuming cuffcompare generates a TMAP and REFMAP file for each input file, does this mean the wrapper tool retrieves only the first and second input files' TMAP and REFMAP files ? Yes, this is the way it works currently. This is clearly problematic, but it meets most users' needs as it enables them to generate a file of combined transcripts--which is needed for Cuffdiff--from many sets of Cufflinks' transcripts. Currently, the Galaxy framework isn't set up to generate multiple outputs for each input; I'm not sure how difficult it will be make these extensions, and it hasn't been a priority as users haven't voiced a need for these files. Of course, contributions are always welcome if you put something together. Best, J. and others are ignored ? Or is there some galaxy black magic python code that iterates multiple inputs and imports them all ? ___ 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] Question about cuffcompare tool implementation
Thanks for the quick answer, Jeremy Goecks wrote, On 04/11/2011 12:50 PM: Assuming cuffcompare generates a TMAP and REFMAP file for each input file, does this mean the wrapper tool retrieves only the first and second input files' TMAP and REFMAP files ? Yes, this is the way it works currently. This is clearly problematic, but it meets most users' needs as it enables them to generate a file of combined transcripts--which is needed for Cuffdiff--from many sets of Cufflinks' transcripts. I'm wondering if users are actually looking into those TMAP REFMAP files, or can they be simply ignored ? Ignoring them would make the tool much simpler (no symlinking patches, etc. ). ___ 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] another update problem
On Mon, Apr 11, 2011 at 7:26 PM, Ryan Golhar golha...@umdnj.edu wrote: I just updated my local galaxy instance using hg pull, and the history items are no longer expandable. What happened? Which browser(s) are affected? I recall reporting some issues with Internet Explorer only and the history peep view not working. 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/
Re: [galaxy-dev] another update problem
This is Safari on Mac OS X. I just reverted to my backup and the problem still exists so I don't know what is going on now. On 4/11/11 2:35 PM, Peter Cock wrote: On Mon, Apr 11, 2011 at 7:26 PM, Ryan Golhargolha...@umdnj.edu wrote: I just updated my local galaxy instance using hg pull, and the history items are no longer expandable. What happened? Which browser(s) are affected? I recall reporting some issues with Internet Explorer only and the history peep view not working. Peter -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. attachment: golharam.vcf___ 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] another update problem
Couple of voodoo things to try: 1. Manually clean the cache of your web browser 2. Restart your apache/nginx Depending on your last update revision, it's possible that some of your javascripts were updated by the latest pull, but your webbrowser maintains a cached older version. Those are the two things I'd try first. Ryan Golhar wrote, On 04/11/2011 02:49 PM: Second problem...Galaxy no longer can determine when a job completes in PBS. I see it submit the job and the paster.log indicates the job ends, but the history display indicates the job hasn't been submitted. On 4/11/11 2:43 PM, Ryan Golhar wrote: This happens in Firefox on Mac as well. On 4/11/11 2:36 PM, Ryan Golhar wrote: This is Safari on Mac OS X. I just reverted to my backup and the problem still exists so I don't know what is going on now. On 4/11/11 2:35 PM, Peter Cock wrote: On Mon, Apr 11, 2011 at 7:26 PM, Ryan Golhargolha...@umdnj.edu wrote: I just updated my local galaxy instance using hg pull, and the history items are no longer expandable. What happened? Which browser(s) are affected? I recall reporting some issues with Internet Explorer only and the history peep view not working. 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/ ___ 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] another update problem
Hi Ryan, I still think it's a javascript problem (most of the fancy DHTML tricks in galaxy, like expanding/collapsing datasets, are done in javascript - so when something like that doesn't work, it's a good place to start). First indication: If you go to your galaxy server with Firefox and open the JavaScript error console, you'll see the following error: = Error: $.jStore is undefined Source File: http://X.X.edu/galaxy/static/scripts/galaxy.base.js?v=8 Line: 1 = Just to be sure, this is not a real galaxy bug, this is a mismatch between what should be the correct javascript and the actual javascript that you are using. So the next step is to see if there are real differences: compare the javascript you have with the one you're supposed to have (if you've updated to the latest galaxy-dist): ## Download your version: $ wget -O galaxy.base.js 'http://X.X.edu/galaxy/static/scripts/galaxy.base.js?v=8' ## Download galaxy's version: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist ## compare them: $ ls -l galaxy.base.js galaxy-dist/static/scripts/packed/galaxy.base.js -rw-r--r-- 1 gordon hannon 8787 Apr 11 16:11 galaxy-dist/static/scripts/packed/galaxy.base.js -rw-r--r-- 1 gordon hannon 9020 Feb 21 13:48 galaxy.base.js = # Obviously, they are not the same. # Assuming wget maintains the file's actual date (Yours is from Feb. 21st), then I can assume you're still using an older version of the javascript file. Perhaps you've pulled but didn't update ? Or merged and took the wrong version ? Check the actual file on your disk to continue and debug it, but IMHO it's definitely a javascript mismatch problem. Hope it helps, -gordon Ryan Golhar wrote, On 04/11/2011 03:13 PM: I restarted the galaxy daemon, apache, and cleared my cache. Still didn't help. I'd be happy to share the URL of my instance via private email if it'll help. On 4/11/11 3:05 PM, Assaf Gordon wrote: Couple of voodoo things to try: 1. Manually clean the cache of your web browser 2. Restart your apache/nginx Depending on your last update revision, it's possible that some of your javascripts were updated by the latest pull, but your webbrowser maintains a cached older version. Those are the two things I'd try first. ___ 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] another update problem
Yeah, I pulled down a new version of galaxy-dist to a new directory and am comparing the differences using diff on my current instance. For some reason hg pull -u didn't work. It aborted because I installed a bam.xml for igv in display_applications/igv. Apparently one was added to galaxy-dist as well. I copied in the new one but now its complaining about some other file. I can't seem to force hg to update so I need to do some of the updating by hand. *** This is not fun *** On 4/11/11 4:19 PM, Assaf Gordon wrote: this is a mismatch between what should be the correct javascript and the actual javascript that you are using. So the next step is to see if there are real differences: compare the javascript you have with the one you're supposed to have (if you've updated to the latest galaxy-dist): -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. attachment: golharam.vcf___ 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] another update problem
I screwed Galaxy. I will delete / reinstall it. At least I will delete it. I think I will revert back to the shell for awhile to get some work done. I've spent *way* too much time trying to get galaxy to work properly. Thanks for all the help everyone. On 4/11/11 4:32 PM, Ryan Golhar wrote: Yeah, I pulled down a new version of galaxy-dist to a new directory and am comparing the differences using diff on my current instance. For some reason hg pull -u didn't work. It aborted because I installed a bam.xml for igv in display_applications/igv. Apparently one was added to galaxy-dist as well. I copied in the new one but now its complaining about some other file. I can't seem to force hg to update so I need to do some of the updating by hand. *** This is not fun *** On 4/11/11 4:19 PM, Assaf Gordon wrote: this is a mismatch between what should be the correct javascript and the actual javascript that you are using. So the next step is to see if there are real differences: compare the javascript you have with the one you're supposed to have (if you've updated to the latest galaxy-dist): ___ 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/ -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. attachment: golharam.vcf___ 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] update probelm...
Hi Liisa, What does hg tip return? K On Mon, Apr 11, 2011 at 10:55 AM, Liisa Koski liisa.ko...@dnalandmarks.ca wrote: Hi I just tried to update my local installation of Galaxy but accidentally hit Ctr-C when it asked me a question added 285 changesets with 649 changes to 354 files local changed static/scripts/packed/jquery.jstore.js which remote deleted use (c)hanged version or (d)elete? interrupted! When I tried to do the update again...it says 'no changes found' But...after restarting my instance...I see that the changes did not get implemented. Is there a way to force this? Thanks in advance, Liisa ___ 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] improved view details button
James Taylor wrote, On 04/11/2011 09:05 PM: Assaf, it should be the last modification to the dataset's metadata, info, etc. Any change that would be made through the edit attributes page. I agree this is confusing and should probably not be shown to the user at all. On Apr 11, 2011, at 7:13 PM, Assaf Gordon wrote: It doesn't give the modification date of the dataset (also: what exactly is modification ? all datasets in Galaxy are immutable). It seems that the modification date is affected by any modification to the history. Just note that changing the history name affects the dataset's modification date. not sure if this is intentional or not - because even conceptually renaming the history doesn't change any metadata of the dataset. ___ 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/
