Trackster displays an error after opening a saved view:
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Error: The requested genome file (/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not be opened. Exiting!
sort: write failed: standard output: Broken pipe
sort: write error
Couldn't open /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len , No such file or directory
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In my universe_wsgi.ini I point to the correct directory where I keep my chrom len files.
# Directory where chrom len files are kept, currently mainly used by trackster
len_file_path = /mnt/referencedata/trackster
This is a bug: Galaxy wasn't using this setting in converters. I've fixed this in -stable changeset 7105c53:
This is a problem between the UCSC chromosome naming convention (e.g., 'chr1') and the Ensembl naming convention (e.g. '1'). In most cases Galaxy handles this transparently, but the new converters do not. This is something that definitely needs to be implemented. Here's a card so that you can follow the feature's progress:
J.