January 2013 - galaxy-dev - lists.galaxyproject.org

Colon in drmout and drmerr file names creates issues with Torque and DRMAA when using 'use_tasked_jobs'.
by Carlos Borroto 18 Jan '13

18 Jan '13

Hi All, Thanks to this email[1] from Peter Cock I was able to find what was causing the error I initially described here[2]. I also now have a theory of why this is happening. My unconfirmed guess. When a colon is present in the standard output or standard error file, someone betweent Galaxy, python-drmaa, pbs-drmaa, Torque or Maui recognize this as a scp syntax, like: user@host:/path/to/file And then choose to at 'galaxy@' in from of what is really a filesystem path. This is why I'm seeing this kind of error: Unable to copy file /var/spool/torque/spool/1013.head.OU to galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9 /task_0/9:1.drmout *** error from copy cp: cannot create regular file `galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0/9:1.drmout': No such file or directory *** end error output Output retained on that host in: /var/spool/torque/undelivered/1013.head.OU By using Peter's ".replace(":", "_")" trick on "lib/galaxy/jobs/runners/drmaa.py" I was able to make this issue go away. As Peter mention this is a very dirty fix and I'm sure there has to be a much cleaner way of fixing this issue. [1]http://dev.list.galaxyproject.org/Galaxy-with-Univa-Grid-Engine-UGE-inste… [2]http://dev.list.galaxyproject.org/Issue-when-enabling-use-tasked-jobs-wit… I'll be opening a ticket on Trello to follow the progress on this issue. Regards, Carlos

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Galaxy Main cloudlaunch stall
by Matthew Shirley 18 Jan '13

18 Jan '13

I've searched the list to see if anyone specifically mentions not being able to use the "cloud launch<https://main.g2.bx.psu.edu/cloudlaunch>" feature on the main public instance, but no one seems to address it. I have no trouble launching Galaxy-cloudman using an AMI and pasting in my own user data. However, I can't successfully use the cloud launch page to do the same. I've tried letting it create a new security group as well as using a pre-existing security group. Also, I've then deleted all security groups to see if it would create one, which it did not. Similarly, I tried creating a new access key pair, with no further success. I make it through the process of entering the key ID and secret key, it pulls existing security group information into the drop-down selector, and I give a cluster name and password and submit the form. Then it just stalls forever. No new security groups and no EC2 instances launched. What is the state of this tool? Thanks.

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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 17 Jan '13

17 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 17 Jan '13

17 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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