July 2011 - galaxy-dev - lists.galaxyproject.org

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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Error when changing default permissions for new histories
by Sarah Diehl 08 Jul '11

08 Jul '11

Hello, when I go to the user preferences and try to change the default permissions for new histories, I always get the following error (full message in attachment): Error - <type 'exceptions.TypeError'>: set_default_permissions() takes exactly 3 non-keyword arguments (2 given) URL: http://solweb2.immunbio.mpg.de/user/set_default_permissions File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) TypeError: set_default_permissions() takes exactly 3 non-keyword arguments (2 given) I would greatly appreciate any help to solve this problem. Thanks in advance! Best regards, Sarah

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Galaxy <-> UCSC Authentication issues
by Federico De Masi 08 Jul '11

08 Jul '11

Dear list, I have recently finished to set local installations of both Galaxy and UCSC servers. Because of the required set-up, access to these is password protected. Galaxy uses the Apache authentication system (as by instructions in galaxy pages) and the username:password combos are the same used by our local UCSC server. Now, whenever I try to export tables to Galaxy from the UCSC hgTables tool, I get the following error on Galaxy: "Dataset generation errors Dataset 33: UCSC Main on Mouse: Rbbp5_Ang2011 (genome) Tool execution generated the following error message: The remote data source application may be off line, please try again later. Error: EOF when reading a line The tool produced the following additional output: Enter username for UCSC-Galaxy at ucsc.cbs.dtu.dk" Similarly, if I try to use UCSC to visualise a track I just created on Galaxy, no track will appear on UCSC I will get this error "Expected 200 http://galaxy.cbs.dtu.dk/display_application/48916fac0de9a85d/ucsc_bigwig/m…: 401 Authorization Required" Did anyone have this issue? How can I solve this? Thanks a lot, Fred -- Federico De Masi, PhD, Assistant Professor The Technical University of Denmark - DTU Center for Biological Sequence Analysis - CBS Kemitorvet 208/002 DK-2800 KGS. LYNGBY, DENMARK Telephone: (+45) 45 25 24 21 Fax: (+45) 45 93 15 85 http://rg.cbs.dtu.dk

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problems with 'Profile Annotations' tool UI
by Hans-Rudolf Hotz 08 Jul '11

08 Jul '11

Hi we are looking into different methods to display dynamic contents in the tool user interface. To start, we looked at the 'Operate on Genomic Intervals:Profile Annotations' tool. We turned it on in a local installation (May 20, "8c11dd28a3cf" release), but we struggled to get the interface to work. On 'http://main.g2.bx.psu.edu/', the tables to choose from are only displayed if there is a history item with: "format: bed, database: hg18". But in our local test installation, we don't get the list of tables, no matter whether we have a ('hg18') bed file in our history or not. It looks like as if the 'from_file="annotation_profiler_options.xml"' statement in the "annotation_profiler.xml" is ignored. I know, the file 'annotation_profiler_options.xml' is read, since I get an error during restart, if I provide invalid xml. Is there anything else, I have to enable, in order to get this interface to work? Currently, I don't care about the tools functionality, I just want the (cool) interface to work. Thank you very much for your help. Regards, Hans PS: this question is connected to Tim's question yesterday - I just should have sent mine first - sorry.

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