- galaxy-dev - lists.galaxyproject.org

Problem uploading to Galaxy
by Andrew Gorzalski 18 Jan '13

18 Jan '13

Hello, I've encountered a problem uploading some .xlsx files to Galaxy. None of the files I've tried uploading today, via html or ftp, have been successfully uploaded. Instead, the box turns grey and says the "Job is waiting to run." If I try to refresh, I get the error: The 'Upload File' tool does not currently support rerunning. Uploading the files to your ftp server and then using "Get file" gives the same result. Any help or suggestions? Andrew Gorzalski

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galaxy using EC2 spot pricing
by Andrew Norman 18 Jan '13

18 Jan '13

Does anyone have any experience running Galaxy using Amazon's EC2 spot pricing? It seems like that could save a lot of money as compared to on-demand pricing, and it appears that there are ways to mix on-demand and spot instances within one processing cluster: http://aws.amazon.com/ec2/spot-and-science/

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missing eye icon on running jobs…
by Langhorst, Brad 18 Jan '13

18 Jan '13

In some cases (e.g. mira) it's nice to be able to follow what's going on in the log file… Does anybody else miss being able to view files as they're running? brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com>

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Workflows
by Neil.Burdett＠csiro.au 18 Jan '13

18 Jan '13

Hi Sorry if these questions are obvious but I just don't know how to find the answers. I'm trying to get one of the API examples to work in http://wiki.galaxyproject.org/Learn/API/Examples . I've got my API key but how do I get/find the workflow id (f2db41e1fa331b3e in the examples). I've created workflow but don't know how to access this key. Also in the first example it states <galaxy_url>/api/workflows However I don't have the "api/workflows" directory structure in my galaxy-dist, do I need to create this? Thanks Neil

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Error trying to remove trackster visualization in latest galaxy-dist
by Anthonius deBoer 18 Jan '13

18 Jan '13

Hi, Tried to remove a trackster visualization in the latest galaxy-dist and got this error: Error Traceback: View as: Interactive | Text | XML (full) ⇝ NameError: global name 'util' is not defined URL: http://srv151/visualization/list?f-sharing=All&sort=-update_time&f-tags=All… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:91 in __call__ view >> return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.framework:94 in decorator view >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.visualization:320 in list view >> ids = util.listify( kwargs['id'] ) NameError: global name 'util' is not defined Extra Features >> Display the lines of code near each part of the traceback Show a debug prompt to allow you to directly debug the code at the traceback Re-GET Page

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Programming error in my new tool for shapeit.
by James Boocock 18 Jan '13

18 Jan '13

ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings. u'UPDATE job SET update_time=?, state=?, stdout=?, stderr=? WHERE job.id = ?' ['2013-01-14 07:17:20.417990', 'error', '', '\n\n\x1b[33mS\x1b[0megmented \x1b[33mHAP\x1b[0mlotype \x1b[33mE\x1b[0mstimation & \x1b[33mI\x1b[0mmputation \x1b[33mT\x1b[0mool\ That is just a sample of the stderr from the galaxy stack trace. I think that shapeit is using 8 bit character codes in the stdout and galaxy is failing on adding to the database. Has anyone experienced this problem and could help me. Cheers James

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Programming error in my new tool shape for shape it
by James Boocock 18 Jan '13

18 Jan '13

ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings. u'UPDATE job SET update_time=?, state=?, stdout=?, stderr=? WHERE job.id = ?' ['2013-01-14 07:17:20.417990', 'error', '', '\n\n\x1b[33mS\x1b[0megmented \x1b[33mHAP\x1b[0mlotype \x1b[33mE\x1b[0mstimation & \x1b[33mI\x1b[0mmputation \x1b[33mT\x1b[0mool\ That is just a sample of the stderr from the galaxy stack trace. I think that shapeit is using 8 bit character codes in the stdout and galaxy is failing on adding to the database. Has anyone experienced this problem and could help me. Cheers James

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Migration of tools
by Joachim Jacob |VIB| 17 Jan '13

17 Jan '13

Hi, Has the devteam a schedule of the order of the tools they plan to migrate to the tool shed? Thanks, Joachim. -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Job output not returned from Cluster
by Sascha Kastens 17 Jan '13

17 Jan '13

Hi all, I have exactly the same problem as described here: http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td879… All the SGE stuff is administrated in our company and unfortunately they know nothing about Galaxy and so it?s my task to get it running. Everything works fine except the problem mentioned above. I?ve contacted Erick but haven?t received a response yet. If anybody can give me some hints where I can look at to solve the problem or at least what I can tell the admins, I would be really grateful. Thanks in advance. If you need further information let me know! Cheers, Sascha

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Tool Error or Bug?
by Elizabeth Clare 17 Jan '13

17 Jan '13

Hi, I cannot determine if I have a tool error or a bug and I am getting errors when I try to report the problem so I am not sure where to send a request for help. I hope i have directed this to the correct place for assistance. I have used Galaxy's main web tools many times successfully so I am familiar with the formats etc. I have now installed Galaxy locally. I successfully uploaded a Fastq file, converted it's format etc. However I cannot get the Fasta manipulation tools to work. When I attempted to use Fasta Width formatter I got the message "dataset_2.dat.Z: No such file or directory /bin/sh: fasta_formatter: command not found" I can't interpret whether that is the file it can't find or the command... it sounds like both? I've had similar errors on the other tools. When I tried to use the bug report to request help I got the error "Mail is not configured for this galaxy instance" so I can't report the problem. I suspect there is something wrong with my local install (are tool installed separately?) but I'd appreciate any insight into the problem or the best place to direct my question. The exact details are as follows: -using new local install (Mac OS 10.8, Python newest version, Galaxy downloaded today) -don't know what an hg pull number is -bug occurred around Thursday at noon (UK time zone) -exact steps, get data to upload a fastq file, convert to fasta, attempt to use fasta width formatter -I've tried to re-upload the file -I've tried the main galaxy server "get data" but it's been stuck at "job waiting to run" for hours so perhaps traffic is heavy. Thanks Beth -- -------------------------------- Dr. Elizabeth L. Clare School of Biological and Chemical Sciences Queen Mary, University of London Mile End Road, London E1 4NS Room 1.02, G. E. Fogg Building e.clare(a)qmul.ac.uk +44 (0)207 882 ext. 5687 School of Biological Sciences University of Bristol, Bristol, UK. Phone: +44 117 954 5909 Website: http://seis.bris.ac.uk/~bzelc/ "If you say yes more often than you say no, you will do interesting things in your life"

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