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

cleanup_datasets.py with postgresql 8.1
by Jennifer Jackson 11 Oct '13

11 Oct '13

Posting to galaxy-dev(a)bx.psu.edu to give the question better exposure to the development community. Please _remove the galaxy-user(a)bx.psu.edu mailing list from all replies_ - we want to avoid double posts. > For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev On 9/26/13 7:29 AM, Malcolm Tobias wrote: > > All, > > My understanding is that the cleanup_datasets.py under > scripts/cleanup_datasets should be compatible with 'older' versions of > postgresql. I'm running 8.1 under CentOS 5. When I attempt to run the > scripts, it fails to clean any data sets. From the logs, I'm noticing > messages like: > > database_connection contains an unknown SQLAlchemy database dialect: > postgresql > > In my universe_wsgi.ini I've defined the database_connection as: > > database_connection = postgresql://galaxy:********@localhost:5432/galaxydb > > and am confident it's working as Galaxy works fine, other than this > problem with deleting older datasets. > > The pgcleanup.py script isn't an option, as it requires postgresql > >=9.1. I noticed yet another version of cleanup_datasets.py under cron > which looks like it might be compatible with postgres, but am leary of > trying it as I'm not sure what it means by "1: database directory to > clean". I'm not sure what directory to point this to, nor am I > confident that just deleting data from the directory is the safest thing. > > Any suggestions on how to proceed? > > Thanks! > > Malcolm > > -- > > Malcolm Tobias > > 314.362.1594 > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

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Solenopsis invicta genome
by patrick.joye＠unil.ch 11 Oct '13

11 Oct '13

Hello, I'm working in the university of Lausanne. We are currently working with fire ants, Solenopsis invicta. I was wondering if that would possible to upload Solenopsis invicta's genome on the Galaxy platform, which could be very useful to us and certainly to other people. Thank you ! Patrick Joye

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masthead and history lost when embedding Galaxy in iframe
by Andy Saurin 11 Oct '13

11 Oct '13

Hi all, I really can't understand why this should be, but in recent versions of Galaxy if you have a simple html page with an iframe embedding Galaxy, you loose the masthead (no login, workflow etc) and the history panel no longer works. eg (newer Galaxy Versions) <iframe src="https://galaxy.cbio.mskcc.org/" width="800px" height="600px"></iframe> <iframe src="https://galaxy.cbio.mskcc.org/" width="800px" height="600px"></iframe> You can see the problems, whereas older versions of galaxy show no problems: <iframe src="http://galaxy.berkeleybop.org:8080/" width="800px" height="600px"></iframe> What could be causing this so that I can try to make amends? Thanks Andy

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Error when running paster directly
by Renato Alves 11 Oct '13

11 Oct '13

Hi everyone, When trying to adapt the init script for debian machines (provided in contrib/) I started playing with paster directly. I was trying to get some sort of help or list of commands/params that can be passed but instead I was presented with the following output: $ python ./scripts/paster.py Usage: ./scripts/paster.py COMMAND Command 'help' not known (you may need to run setup.py egg_info) Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/home/galaxy/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 367, in run commands = get_commands().items() NameError: global name 'get_commands' is not defined After inspection of the file, the get_commands function doesn't seem to be defined nor imported. I'm not sure how to proceed at this point. Thanks, Renato

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Unicode in tool stderr crashing galaxy?
by Guest, Simon 10 Oct '13

10 Oct '13

My optimism was short lived. I think I've hit a galaxy bug in Unicode processing. Having managed to get the deseq tool not to crash galaxy in the sqlalchemy layer, I now get a crash when clicking on the info->stderr for the tool output dataset, probably because it contains Unicode. Here's the traceback from paster.log: ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 47124) Traceback (most recent call last): File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib64/python2.6/SocketServer.py", line 617, in __init__ self.handle() File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 442, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib64/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 437, in handle_one_request self.wsgi_execute() File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 290, in wsgi_execute self.wsgi_write_chunk(chunk) File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 150, in wsgi_write_chunk self.wfile.write(chunk) File "/usr/lib64/python2.6/socket.py", line 316, in write data = str(data) # XXX Should really reject non-string non-buffers UnicodeEncodeError: 'ascii' codec can't encode character u'\u2018' in position 169: ordinal not in range(128) ---------------------------------------- I don't know where to look to find the actual stderr output. Any pointers? Is this actually a galaxy bug now? cheers, Simon ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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Frames issue with tool shed README links?
by Peter Cock 10 Oct '13

10 Oct '13

Consider the following sequence: 1. Goto http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan 2. The README file explains this is for InterProScan 4, and has a link to http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5 for Bjoern's InterProScan 45 wrapper. 3. Click the link for InterProScan 5. 4. Notice the link opened within the frame, and you now have a nested tool shed menu. 5. Click on the link to InterPro itself, http://www.ebi.ac.uk/interpro/interproscan.html 6. Notice the double nested frame remains, and now the InterPro page is squeezed into the bottom left. ----- This isn't specific to these repositories, e.g. 1. Goto http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go 2. The README file introduction refers to the tool being available on the main tool shed, "It is available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go " 3. Click on that link 4. Observe a double nested tool shed interface, with the Test Tool Shed at the top, and the Main Tool Shed nested within. ----- Suggested fix: All links within Tool Shed README files should be modified to open full frame by adding target="_top" to them. Peter

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UCSC Main table browser invalid link
by Gonsky, Rivkah, Ph.D 10 Oct '13

10 Oct '13

Link doesn't work Rivkah Gonsky Inflammatory Bowel and Immunobiology Research Institute Davis 4063 8700 Beverly Blvd Los Angeles, CA 90048 310-423-7624 gonsky(a)cshs.org<mailto:gonsky@cshs.org> IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED. If you have received this message in error, please notify us immediately by calling (310) 423-6428 and destroy the related message. Thank You for your cooperation.

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Dealing with cluster job preemption
by Sytchev, Ilya 10 Oct '13

10 Oct '13

Hi, Our Galaxy instance is configured to use LSF. The problem is that sometimes our jobs get preempted (stopped and re-queued to let higher-priority jobs run) and Galaxy thinks that those jobs have failed. Is there any way around that by any chance? Thanks, Ilya

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FASTQ converter not working
by James Tarver 10 Oct '13

10 Oct '13

So I have used Galaxy to convert >50 different FASTQ files into FASTA with no problems before over the past year. The sequencer and FASTQ file format have been identical, however, yesterday when I tired to use the the FASTQ to FASTA converter I couldn't get it to recognise my files. The drop down 'FASTQ Library to convert:' tab was empty and unable to select the dataset to convert I then switched histories to one where this action had already been done to repeat it and make sure it was nothing odd with the file I uploaded. However, again the tab was empty and I was unable to select the file to convert. Suggestions? JT

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Visualizations broken after Aug. 12 update
by Liisa Koski 10 Oct '13

10 Oct '13

Hello, We recently updated to the Aug.12 distribution. I u commented the visualizations_config_directory = config/visualizations in the universe file and when I restarted and tried to view past Trackster Visualizations none of my tracks load. I get the error displayed in the track itself: Cannot display dataset due to an error. View error. Try again. When I click on View error I get pop up with this for my gff3 track: Input error: Cannot split into blocks. Found interval with fewer than 12 columns. needLargeMem: trying to allocate 0 bytes (limit: 17179869184) With this for my BAM track: grep: /Galaxy/galaxy_dist/database/files/016/dataset_16392.dat: No such file or directory needLargeMem: trying to allocate 0 bytes (limit: 17179869184) All tracks in all published Visualizations are no longer loading. I do not see any errors in the log files. I have also updated my datatypes.conf file by copying over datatypes.conf.sample Any help would be much appreciated. Thanks in advance, Liisa

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