June 2012 - galaxy-dev - lists.galaxyproject.org

FastQC Tool Errors
by Josh Nielsen 02 Jul '12

02 Jul '12

Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: "Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: " And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: "Exception in thread "main" java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.<init>(Window.java:437) at java.awt.Frame.<init>(Frame.java:419) at java.awt.Frame.<init>(Frame.java:384) at javax.swing.JFrame.<init>(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102)" Both errors seem to have something to do with the graphical GUI component of FastQC (which I have seen some screenshots for on the FastQC webpage). If this application is GUI-driven how did the online PSU Galaxy get it to work with their wrapper script when the tools are run in a command-line environment with no X11 or Gtk? Essentially I'm just wondering what steps I'm missing here to getting this to work with our Galaxy mirror, other than just dropping the executable in place? Any suggestions? Thanks, Josh

3 7

ValueError: Maximum key size is 448 bits
by Sajoscha Sauer 02 Jul '12

02 Jul '12

Hi, I have updated our development installation of Galaxy. This wasn't done for a long time, so it was a quite old version. The update is done from galaxy-central. I did hg pull, hg update and a db update. All that without errors. But when I now try to start Galaxy, I get the following: … Traceback (most recent call last): File "/galaxy-dev/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/galaxy-dev/lib/galaxy/app.py", line 71, in __init__ self.security = security.SecurityHelper( id_secret=self.config.id_secret ) File "/galaxy-dev/lib/galaxy/web/security/__init__.py", line 36, in __init__ self.id_cipher = Blowfish.new( self.id_secret ) ValueError: Maximum key size is 448 bits I'm totally lost on this one. Does anyone have an idea or a hint on where to start? It would be highly appreciated! Thanks a lot! Sajoscha

1 1

Where is the data and program
by bluesky8640 30 Jun '12

30 Jun '12

Dear all, I have done some exercises on galaxy, and i want to run these exercises on our own workflow system to make some comparison. How can i find the input data and program of the exercises in galaxy? Meanwhile, I am trying to learn galaxy, does anyone have some papers about the design and implementation of galaxy? Thank you in advance, Jin

1 0

Re: [galaxy-dev] BAM format question
by Jennifer Jackson 29 Jun '12

29 Jun '12

Hello Susan, A BAM file is in binary format. To understand this datatype, please see the documentation for the tools in the group "SAM Tools". To view the data in a human-readable text file, convert using the tool "BAM to SAM". More information about the type: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002/ The best way to view this data is in a viewer such as Trackster or one of the alternatives listed in the dataset's box. Once you have a database assigned, the options will be listed. Hopefully this helps. It would be helpful to please direct questions to the mailing list so that our entire team & community can contribute to and benefit from replies, Jen Galaxy team On 6/29/12 9:44 AM, Susan Hester wrote: > > Hi, > > Yes I am registered now. I ran the tutorial exercise on the Galaxy > datset / Tophat and tried to view it gave me an error and said the BAM > file was not a valid file for Win32.? > > Any ideas? > > Susan Hester, Ph.D. > Research Biologist > Systems Biology Branch > Integrated Systems Toxicology Division (ISTD) > National Health and Environmental Effects Research Lab > US Environmental Protection Agency > 109 T.W. Alexander Dr. > MD-B143-06 > Research Triangle Park, NC 27711 > hester.susan(a)epa.gov > > Inactive hide details for Jennifer Jackson ---06/29/2012 12:13:36 > PM---Hello Susan, Are you still having problem with registratJennifer > Jackson ---06/29/2012 12:13:36 PM---Hello Susan, Are you still having > problem with registration? > > From: Jennifer Jackson <jen(a)bx.psu.edu> > To: Susan Hester/RTP/USEPA/US@EPA > Cc: galaxy-dev(a)lists.bx.psu.edu > Date: 06/29/2012 12:13 PM > Subject: Re: [galaxy-dev] (no subject) > > ------------------------------------------------------------------------ > > > > Hello Susan, > > Are you still having problem with registration? > > Please try again, doing the following to register at the Galaxy main > public instance. > - Start at: _http://usegalaxy.org/_ > - This will take you to: _https://main.g2.bx.psu.edu/_ > - On the top menu, far right, is the "User" menu. Click on this, there > are two options, "register" is the second. > > Best, > > Jen > Galaxy team > > On 6/28/12 1:51 PM, Susan Hester wrote: > > > Hi, > > I'm trying to register in Galaxy on the public server and under > the "user" tab "register" is greyed out? How do I register? > > Susan Hester, Ph.D. > Research Biologist > Systems Biology Branch > Integrated Systems Toxicology Division (ISTD) > National Health and Environmental Effects Research Lab > US Environmental Protection Agency > 109 T.W. Alexander Dr. > MD-B143-06 > Research Triangle Park, NC 27711_ > __hester.susan(a)epa.gov_ <mailto:hester.susan@epa.gov> > > > ___________________________________________________________ > 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/_ > > > -- > Jennifer Jackson > _http://galaxyproject.org_ <http://galaxyproject.org/> > > -- Jennifer Jackson http://galaxyproject.org

1 0

Get bai file for tool-input bam file
by Geert Vandeweyer 29 Jun '12

29 Jun '12

Hi, I'm working on a tool that will export vcf files together with bam/bai files to a long term storage location on our local installation. How can i get the path to the automatically created bai file for a provided bam file? Can it be derived from the file bam file path? Best regards, Geert Vandeweyer -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

2 1

(no subject)
by Susan Hester 29 Jun '12

29 Jun '12

Hi, I'm trying to register in Galaxy on the public server and under the "user" tab "register" is greyed out? How do I register? Susan Hester, Ph.D. Research Biologist Systems Biology Branch Integrated Systems Toxicology Division (ISTD) National Health and Environmental Effects Research Lab US Environmental Protection Agency 109 T.W. Alexander Dr. MD-B143-06 Research Triangle Park, NC 27711 hester.susan(a)epa.gov

2 1

July 2012 Galaxy Update
by Dave Clements 28 Jun '12

28 Jun '12

Hello all, The July 2012 Galaxy Update is now available<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07>. *Highlights:* - GCC2012 is July 25-27!<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#GCC2012_is_July_25-27.21> - Register by July 18<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register> - Other Upcoming Events and Deadlines<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Upcoming_Events_and_Deadlin…> ,* including these deadlines in the next several days* - Galaxy Workshops in South Africa<http://wiki.g2.bx.psu.edu/News/GalaxyWorkshopsInSouthAfrica>(deadline: *June 30*) and the South African Genetics & Bioinformatics Society Conference <http://genetics.cmc-uct.co.za/> (deadline *July 1*) - Systems Bioinformatics Workshop<http://gaggle.systemsbiology.net/workshop2012/>(deadline: *June 30*) - GMOD Summer School<http://gmod.org/wiki/2012%20GMOD%20Summer%20School>(deadline: *July 9*) - 31 New Papers<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#New_Papers>, including two new *Current Protocols* - Open Positions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Who.27s_Hiring>at six different institutions - Tool Shed Contributions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Tool_Shed_Contributions> - A new CloudMan distribution was released last month<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#New_Distributions> - Plus <http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Other_News> - Easily wrap your R functions as Galaxy tools - help schedule the first GalaxyCzars<http://wiki.g2.bx.psu.edu/Community/GalaxyCzars>conference call on July 9 or 10 - and lots of new screencasts, tutorials, and new genomes on main If you have anything you would like to see in the August *Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates> *, please let me know. Thanks, Dave Clements -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

1 0

Port Config SMTP Server
by CHEBBI Mohamed Amine 28 Jun '12

28 Jun '12

Hi Galxy-team ! I have to use the smtp-server in Galaxy. However I don't see how to set the port to 587 in the universe_wsgi.ini to enable sending mails from my own server. I saw the documetation but I didn't find any response for this. Thank-you in advance for your help. Regards Amine

2 2

tuple unpack error during tool install
by Langhorst, Brad 28 Jun '12

28 Jun '12

I found the problem with my blocked cookies, now I encounter a new error. File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 291 in install_repository description, repository_clone_url, changeset_revision = repo_info_tuple ValueError: too many values to unpack repo_info_tuple returns more than 3 items? Is this a known bug? Did I make some error? here's the full log output 172.17.130.187 - - [28/Jun/2012:14:09:58 -0400] "POST /admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=74 41a94a254875fe3e3519ca4cd7ade4305e8b8f%3A7b2264776773696d223a205b2247656e65726174652073696d756c617465642072656164732066726f6d20612066617374612073657175656e6365 207573696e672064776773696d222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f64776773696d222c20223531323637313 63034626162222c202231225d7d&includes_tools=True HTTP/1.1" 500 - "http://galaxy.neb.com/admin_toolshed/install_repository?tool_shed_url=http:… u.edu/&repo_info_dict=7441a94a254875fe3e3519ca4cd7ade4305e8b8f:7b2264776773696d223a205b2247656e65726174652073696d756c617465642072656164732066726f6d206120666173 74612073657175656e6365207573696e672064776773696d222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f64776773696 d222c2022353132363731363034626162222c202231225d7d&includes_tools=True" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.1 (KHTML, like Gecko) Ch rome/22.0.1189.0 Safari/537.1" Error - <type 'exceptions.ValueError'>: too many values to unpack URL: http://galaxy.neb.com/admin_toolshed/install_repository?tool_shed_url=http%… e4305e8b8f%3A7b2264776773696d223a205b2247656e65726174652073696d756c617465642072656164732066726f6d20612066617374612073657175656e6365207573696e672064776773696d22 2c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f64776773696d222c2022353132363731363034626162222c202231225d7d& includes_tools=True File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response ) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 291 in install_repository description, repository_clone_url, changeset_revision = repo_info_tuple ValueError: too many values to unpack Brad -- Brad Langhorst langhorst(a)neb.com 978-380-7564

2 4

error when accessing toolshed
by Langhorst, Brad 28 Jun '12

28 Jun '12

When i try to install a tool from the main toolshed i see this error Not Found The resource could not be found. No route for /repository/Noneadmin_toolshed/install_repository I see in the archive that there was a problem but Greg fixed it.. http://dev.list.galaxyproject.org/Toolshed-not-accessible-td4096102.html I think i have this changeset he refers to... hg transplant -s https://bitbucket.org/galaxy/galaxy-central -m 255f4bde822b searching for changes skipping already applied revision 6333:255f4bde822b Here's my tool_sheds_conf.xml <?xml version="1.0"?> <tool_sheds> <tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/> <tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/> </tool_sheds> Did I misconfigure something? Thanks for any hints... brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com> 978-380-7564

2 2