Re: [galaxy-user] Most Popular Linux flavour for Galaxy
I have instances running on RHEL 5 and CentOS 5 and never had any OS-specific issues, works great. -Leandro On Tue, Jun 7, 2011 at 4:45 PM, Nate Coraor wrote: > Matloob Khushi wrote: >> Hello Galaxy Users >> >> We are anticipating setting up a local instance of Galaxy and wondering what >> is the most popular (or best) flavour of Linux people out there using. >> >> I wonder which OS on UseGalaxy.org has been used. Thanks for your help. > > Hi Matloob, > > The public Galaxy server runs Solaris 10. The tools run on two > clusters, one running Debian Squeeze and the other running RHEL 5.6, > both amd64. > > You might find that a specialized distribution like BioLinux or > Scientific Linux may pre-package many of the tools you're interested in, > which would make setup a bit easier. > > --nate > >> >> Regards >> Matloob >> PhD Candidate > >> ___ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ > > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] [galaxy-dev] Peep view for history elements broken on IE?
Hi, In IE go to Tools -> Internet Options -> Advanced Tab, then under Browsing section: - Uncheck "Disable Script debugging (Internet Explorer) - Uncheck "Disable Script debugging (Other) - Check Display a notification about every script error Then you will see the Javascript error when you try to reload the Galaxy page and then try to expand a history item. I would help debug the Galaxy IE issues but I am at work and cannot change these settings on my work computer (the are grey out :( ) -Leandro On Mon, Jan 31, 2011 at 12:44 PM, Peter wrote: > > On Thu, Jan 27, 2011 at 6:07 PM, Kanwei Li wrote: > >> > >> Weird.. the proxy shouldn't be relevant. Could you open the javascript > >> error console and see what the error is? > >> > > OK - but how? There is no sign of a javascript error... > > I've been to menu Tools / Internet Options... / Advanced tab, > then under the "Browsing" category unchecked the box that says > "Disable Script Debugging" (to enable debugging), and also > checked "Display a notification about every script error". I still > don't see any javascript error when using Galaxy. > > I've tried following http://www.phpied.com/javascript-console-in-ie/ > e.g. putting javascript:debugger; in the URL box will bring up the > debugger - but then what? > > On Mon, Jan 31, 2011 at 11:14 AM, Leandro Hermida > wrote: > > Hi everyone, > > > > I posted a similar thread back in August > > > > http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-August/003224.html > > > > There are a couple web UI issues with Galaxy when using IE, like as > > mentioned in this thread in the history pane data items the link is > missing > > and you cannot expand them to "peep" at what's there. > > Glad to know its not just our setup where the peep links don't work on IE7. > > Thanks! > > Peter > ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Re: [galaxy-user] Peep view for history elements broken on IE?
Hi everyone, I posted a similar thread back in August http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-August/003224.html There are a couple web UI issues with Galaxy when using IE, like as mentioned in this thread in the history pane data items the link is missing and you cannot expand them to "peep" at what's there. -Leandro On Thu, Jan 27, 2011 at 6:07 PM, Kanwei Li wrote: > Weird.. the proxy shouldn't be relevant. Could you open the javascript > error console and see what the error is? > > On Thu, Jan 27, 2011 at 8:57 AM, Peter > wrote: > > On Wed, Jan 26, 2011 at 7:49 PM, Kanwei Li wrote: > >> Hi Peter, > >> > >> Is this still an issue? The error you describe sounds like a jStore > >> problem but I tested it in IE7 and it works. > >> > >> Thanks, > >> > >> Kanwei > > > > Hi Kanwei, > > > > I just tried the public Galaxy at http://usegalaxy.org aka > > http://main.g2.bx.psu.edu/ and also ttp://test.g2.bx.psu.edu/ which > > says it tracks the galaxy-central repo, and for both the history peep > > links don't work. This is using Internet Explorer version 7.0.5730.13, > > which I believe is the current release (from back in 2007), from two > > different Windows XP machines at our institute (which are accessing > > the internet via a proxy - perhaps relevant?). > > > > Peter > > > ___ > galaxy-user mailing list > galaxy-user@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user > ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Re: [galaxy-user] parallel processing of multiple files on a multi-processor box?
Hi Yury, My apologies if I missed something or misunderstood you question, but I am not sure the IT group is correct saying Galaxy won't be able to utilize multiple processors on an SMP box. When running a tool the Galaxy server will fork off an asynchronous sub process, and if you run that tool multiple times in your user session in parallel it will have that many sub processes running in parallel and on an SMP box the kernel will properly utilize the available CPUs. So you would upload the 6 FASTQ files into your history and then you would run Groomer on each (you don't have to wait for one to finish in order to launch the next) and then the same for Bowtie. hth, Leandro On Mon, Jan 3, 2011 at 10:52 PM, Yury Bukhman wrote: > Hi, > > I have an RNA-seq study with 6 runs. The output is 6 Illumina fastq files. > I would like to be able to run FASTQ Groomer and Bowtie on all 6 in > parallel, utilizing a multi-processor box. Is this possible? It appears > (to our IT group) that Galaxy won't be able to utilize multiple processors > on an SMP box for the same user session, and we would need to set up a > cluster to do things like this. Is this so? Is there a work-around? > > Thanks. > > Yury > > ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
