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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