Visualizations broken after Aug. 12 update
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
You'll need to do two things: (1) Install wigToBigWig and bedtools; see steps 2 and 3 here: http://wiki.galaxyproject.org/Visualization%20Setup (2) Update your datatypes_conf.xml file: If you haven't made changes to your datatypes_conf.xml file, you can just copy datatypes_conf.xml.sample to datatypes_conf.xml to get the needed converters. If you've made changes to datatypes_conf.xml, you'll need to manually add the needed converters. We recently transitioned all the *_to_summary_tree converters to *_to_bigwig, so you'll want to remove the summary_tree converters and replace them with the bigwig converters. Let us know if you have any problems/questions. Best, J. On Oct 3, 2013, at 1:33 PM, Liisa Koski wrote:
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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Thank you Jeremy, It turned out the issue was our version of bedtools. We updated to 2.17.0 and no longer have the errors. Cheers, Liisa From: Jeremy Goecks <jeremy.goecks@emory.edu> To: Liisa Koski <liisa.koski@basf.com> Cc: "galaxy-dev@lists.bx.psu.edu Galaxy-dev" <galaxy-dev@lists.bx.psu.edu> Date: 05/10/2013 08:08 PM Subject: Re: [galaxy-dev] Visualizations broken after Aug. 12 update You'll need to do two things: (1) Install wigToBigWig and bedtools; see steps 2 and 3 here: http://wiki.galaxyproject.org/Visualization%20Setup (2) Update your datatypes_conf.xml file: If you haven't made changes to your datatypes_conf.xml file, you can just copy datatypes_conf.xml.sample to datatypes_conf.xml to get the needed converters. If you've made changes to datatypes_conf.xml, you'll need to manually add the needed converters. We recently transitioned all the *_to_summary_tree converters to *_to_bigwig, so you'll want to remove the summary_tree converters and replace them with the bigwig converters. Let us know if you have any problems/questions. Best, J. On Oct 3, 2013, at 1:33 PM, Liisa Koski wrote: 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 ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
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Jeremy Goecks -
Liisa Koski