>> Trackster displays an error after opening a saved view:
>>
>> ***********************
>> 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
>> ***********************
>>
>> 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:
https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a3714bc117118989712a2
> Further, I had to remove the 'chr' in the chrom len files to make it work.
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:
https://trello.com/c/lai0uU9g
Best,
J.
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