- galaxy-dev - lists.galaxyproject.org

Galaxy @ ISMB/ECCB, 3DSIG, and BOSC
by Dave Clements 12 Jul '11

12 Jul '11

Hello all, Galaxy will have a large presence at ISMB/ECCB, 3DSIG, and BOSC, all of which start this week in Vienna. Galaxy related content includes (at least): 1 Galaxy organized workshop on "Genomics for Non-Model Organisms" featuring 4 talks, 7 additional talks at ISMB/ECCB and BOSC, and 3 Posters at ISMB/ECCB and 3DSIG That's enough to fill a wiki page and a flier (and so it has :-). See http://wiki.g2.bx.psu.edu/Events/ISMB-ECCB-BOSC%202011 for a listing of all known Galaxy-related content and a flyer you can print out and take with you. Watch Twitter (@galaxyproject, #usegalaxy) during the conference for updates and reminders. Thanks, Dave C. -- http://getgalaxy.org http://usegalaxy.org/ http://galaxyproject.org/wiki

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Tool Shed Problem
by SHAUN WEBB 12 Jul '11

12 Jul '11

Hi Galaxy team, I created a new repository on the tool shed called "test", I wanted to see what steps were required to publish a tool before I go ahead and release the production version. I then tried to change the name of the repository and got a server error. When I search for test, try to navigate to 2nd page of the repository list or view my own repositories the server error occurs. Apologies if I broke it... On a side note, I did not see an option to delete a created repository. Also, my test repository went live straight away. Would it make sense to be able to create a repository and load files then have a publish button for when you choose to release. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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how to reduce Load of galaxy in standalone system by python
by shashi shekhar 12 Jul '11

12 Jul '11

Hi All, i have system with single cpu . and have installed galaxy .while running galaxy it will create high load on system. how are you reducing the load of galaxy in system by using the python . Regards shashi

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Add Genome
by Somayyeh Fahiminiya 12 Jul '11

12 Jul '11

Hello everyone, Could you plz add the genome of "*Brachypodium distachyon*" to the Galaxy. Thanks in advance

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BAM display at Trackster
by Vipin TS 12 Jul '11

12 Jul '11

Hi Galaxy team, I am experiencing a problem with visualizing my BAM files through Trackster at my Galaxy instance. Please find the attached image along with this mail. >From the log file I am not seeing any clues about the error message which is displayed on my browser page (A dependency (bai) was in an error state.) I updated my instance recently, It will be great if you can help me on the same. Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Tuebingen

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TopHat V1.1 with GTF files
by Chorny, Ilya 11 Jul '11

11 Jul '11

I was wondering how to pass a GTF file to the current Tophat implementation in Galaxy. It says that -G/--GTF is an implemented parameter but that option does not show up. BTW, what version of tophat is supplied with the most recent stable release. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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Handling runner-specific (SLURM) DRMAA settings
by Roman Valls 11 Jul '11

11 Jul '11

Hello hitchikers, Together with some people here at UPPMAX, Stockholm, we're trying to code proper support for SLURM via DRMAA on Galaxy. Thanks to Martin, we've managed to make it work so far, not without putting some intrusive burden into it (see pic attached). The memory allocation is not something the average user really needs, so we can take the radio buttons away and assume "reasonable defaults" (i.e go with job manager's defaults). Some goes for the core granularity, which is ok in most cases (sending tool jobs to individual CPU cores instead of whole nodes). The only "problems" are time allocation and project id's. The first helps the job manager on better scheduling, the latter is how we partition research projects (budgeting and core hours allowed per project). The general config file allows us to set a fixed project: default_cluster_job_runner = drmaa://-A a2010002 -p core And even set per-tool job settings. But we would like each user to have the ability to change those settings. What is the least intrusive way to set per-user native (site-specific) job manager settings ? Which classes/scripts should we look at/tweak/extend ? Thanks in advance ! Martin and Roman

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Galaxy Has a New Wiki
by Dave Clements 10 Jul '11

10 Jul '11

Hello all, It is my pleasure to announce that Galaxy has a new wiki: http://galaxyproject.org/wiki. This wiki contains all the content from the old bitbucket wiki, plus a bunch of new content (most of which is still work in progress). The new wiki is based on MoinMoin and includes several new or improved features: * Search! * an automatically generated list of all pages (click on All Pages in sidebar) * Ability to upload files and images without using Mercurial. * plus a lot more The content, organization, and look and feel haven't entirely settled yet, so expect things to move around for a bit. You don't need any special knowledge to read the wiki. If you want to update the wiki you'll need to create a login (click on the Login link). Anyone can create a login, but you will need to answer a random (but hopefully easy) question about Galaxy to do so*. You can use either MoinMoin markup or Creole markup (but not both on the same page). We are hoping that the new wiki will be both much easier to use and to update than the old one. If you have any questions or comments, please send them to me or to the list as appropriate. Look for more emails as more features in the wiki become fully functional. Thanks, Dave C. * And you will be asked to answer questions every time you update pages. If you get tired of this (and you will), please send me your wiki login and I will make those annoying (but spam-preventing) questions go away. -- http://getgalaxy.org http://usegalaxy.org/ http://galaxyproject.org/wiki

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Re: [galaxy-dev] admin users
by Yann Surget-Groba 09 Jul '11

09 Jul '11

Hi Ross, thanks that was the problem, it works fine with no space. I'll raise a ticket about it. yann On 07/08/2011 04:29 PM, Ross wrote: > I seem to remember being bitten by this once years ago when I had > spaces between the comma and the next email address - but I never > fixed it - someone else may have. > If that turns out to be your problem please raise a ticket since it > means the parsing is wrong - spaces should be ignored around the comma > delims. > > On Sat, Jul 9, 2011 at 2:50 AM, Yann Surget-Groba<ysurgetg(a)ucsc.edu> wrote: >> Dear All, >> >> I have a local galaxy instance and I have problems with admin users. I have >> a comma separated list of valid galaxy users in the universe_wsgi.ini file >> but only the first one has access to the admin tab, it doesn't appear for >> the other ones. >> Am I missing something? >> Thanks in advance, >> Yann >> >> ___________________________________________________________ >> 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/ >> > >

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admin users
by Yann Surget-Groba 08 Jul '11

08 Jul '11

Dear All, I have a local galaxy instance and I have problems with admin users. I have a comma separated list of valid galaxy users in the universe_wsgi.ini file but only the first one has access to the admin tab, it doesn't appear for the other ones. Am I missing something? Thanks in advance, Yann

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