- galaxy-dev - lists.galaxyproject.org

deleted_new kills handlers
by Ido Tamir 22 Jan '13

22 Jan '13

Dear galaxy maintainers, we have the problem that killing jobs running on drmaa before they run leading to a deleted_new state, kills our handlers (sometimes?). The job gets sent to the handler, but the handler never acknowledges the jobs (local and drmaa) and all submitted jobs afterwards stay in submitted state. Normally submission works fine, running also. Is such a problem known to anybody else? in my universe_wsgi.ini: enable_job_recovery = False I don't know which other settings could affect this. Could it be an old drmaa library, maybe because the SGE was updated after galaxy installation? Other ideas? thank you very much, ido

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Redirecting to a URL and breaking the frameset
by Paul Boddie 22 Jan '13

22 Jan '13

Hello, Is there a convenient recipe for redirecting to a URL and breaking the frameset? I have been trying to use trans.response.send_redirect with a variety of URLs, either something as simple as url_for("/") or as complicated as a url_for invocation with lots of arguments, but the resulting content produced for the centre frame is always confined to the centre frame and always includes the top navigation bar. I suppose an alternative query would concern whether it is possible to disable the navigation bar when redirecting within the centre frame, but I actually want to update the user information in the navigation bar. Paul

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Upload file from url
by Zinonas Antoniou 21 Jan '13

21 Jan '13

Hello, I want to upload a file from a script. A user will select a file, and the full path of the file will be saved, like http://www.example.com/myfile.csv I want to run the upload module of galaxy to save this file from the http path to galaxy. Do you have any suggestions please? Thank you in advance, Zinon

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Visualise Galaxy workflows using graphviz
by Peter van Heusden 21 Jan '13

21 Jan '13

Hi there Because my Galaxy workflows tend to sprawl outside the viewable space in my browser, I've written a script that, when given a workflow JSON file as input, writes out a graphviz dot format graph of the workflow. By default the graph treats datasets as nodes and analyses as edges (unlike the Galaxy workflow editor, but quite like the way the history is presented), but you can choose to have analyses as nodes (and thus datasets as edges) too. In case anyone else finds this useful, the code can be downloaded from my bitbucket: https://bitbucket.org/pvanheus/galaxy/src/f29453f3d9d8/contrib/workflow_to_… Usage is something like: ./workflow_to_dot.py Galaxy-Workflow.ga |dot -Tsvg >workflow.svg and then you can view your workflow.svg with eog or another viewer. Peter

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NameError in update_manager.py
by Anthonius deBoer 19 Jan '13

19 Jan '13

Hi, I am seeing this in the log files when I start up... It seems to identify a name error in the file update_manager.py I am not sure if it is related, but some of my manager processes are just dying without any errors in the log...The processes are just killed (The PID is just gone, so run.sh --stop_daemon tells me they are not valid).... I did notice that python library is /usr/lib64/python2.6/threading.py, but I am using a virtual_env installation so I would have assumed it would have been using the lib64 stuff in my virtual_env environment, but then again, there is no file threading.py in that library so I guess it is not making a complete copy of all the files... In any case, my galaxy system is very unstable, so any help would be appreciated... Thon galaxy.tool_shed.update_manager INFO 2013-01-19 12:19:02,167 Update manager restarter starting up... Exception in thread Thread-1: Traceback (most recent call last): File "/usr/lib64/python2.6/threading.py", line 532, in __bootstrap_inner self.run() File "/usr/lib64/python2.6/threading.py", line 484, in run self.__target(*self.__args, **self.__kwargs) File "/mnt/ngs/analysis/svcgalaxy/galaxy-dist/lib/galaxy/tool_shed/update_manager.py", line 25, in __restarter .filter( and_( self.app.model.ToolShedRepository.table.c.update_available == False, NameError: global name 'and_' is not defined galaxy.datatypes.registry DEBUG 2013-01-19 12:19:02,175 Loaded display application 'ucsc_bam' for datatype 'bam', i

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local install problem with fasta manipulation tools?
by elclare.evol.biology＠gmail.com 19 Jan '13

19 Jan '13

Hi I hope I have the correct place to ask for assistance. I've been trying to use a local install of Galaxy. I can upload data and convert formats (FASTq to FASTA) but can't use fasta manipulation tools like width formatter or collapse. I am told "No such file or directory /bin/sh: fasta_formatter: command not found". I don't see these in the list of tools with dependencies. I've used them frequently on the public website so I don't think this is a problem of my file formats. What am i missing? When I try to send a bug report through the local I get an error that mail is not configured. I assume i have not conducted the installation properly but I can't figure out what i have done wrong. I tried to do the local install because my files on the web version have been sitting for many hours waiting to run. Thanks for any help. Beth

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UCSC Data Browser
by Robert Chase 19 Jan '13

19 Jan '13

Hello, Is anyone having trouble with the UCSC data browser? I got the following from one of my users: Hi guys, I try to fetch data from UCSC browser. A summary of my query shows that I am getting what I ask for, but when I "Send the data to Galaxy" I am returned to the channing galaxy home page and the data never appears in the history. When I use public instance, it all works. Not sure where the disconnect is. Thanks Any help would be appreciated. -Rob

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login problems
by Solorzano, Eleanne 18 Jan '13

18 Jan '13

Hello, I am trying to connect to ftp with my username and password that I registered in galaxy. I am doing this through Filezilla. I am getting the error "could not connect to server". Do you know what the problem is, please? Thank you. Eleanne

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Integration of STAR Aligner v2.2.0c into Galaxy
by Sorn, Patrick 18 Jan '13

18 Jan '13

Hi all, I want to integrate STAR Aligner v2.2.0c into Galaxy and I was wondering if anyone else is working on this? If nobody is, I would do this. Best regards, Patrick Sorn

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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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