- galaxy-dev - lists.galaxyproject.org

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

Galaxy can't find valid files in user folder
by Ciara Ledero 02 Jul '12

02 Jul '12

Hi all, My apologies for reposting this, but I thought I ought have asked this in a separate thread instead of appending it to a previous message. Anyway, I was able to set up a folder for a user (in my case, my own non-admin user account). universe_wsgi.ini's been configured to allow users to utilize a data library. I've also created a library for my non-admin user account. When all was set, I tried uploading a file to the library. But Galaxy prompted me that the folder did not contain any valid files. I thought I provided the wrong path; I even thought I really did not put anything in the folder. But when I checked, every thing seemed fine. I'm really stumped. I've searched the mailing list and even the wiki, and unfortunately I was not able to find a decent answer. I changed the file extension to .fastq and I indicated that the file to be uploaded was a FASTQ one, as Jen has suggested. I still got the same error in the end. I've scanned the universe_wsgi.ini file to see if there's anything else that I needed to configure, but I found none. Thanks in advance for your help! CL

1 0

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