Trackster error: not able to find the chrom len file
Dear all, I updated to the latest Galaxy stable code, and updated the datatypes_conf.xml. 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 Thanks for any advice, Cheers, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
I just have symlinked the files to the right location. Is this the correct solution? Further, I had to remove the 'chr' in the chrom len files to make it work. Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 06/11/2013 03:26 PM, Joachim Jacob | VIB | wrote:
Dear all,
I updated to the latest Galaxy stable code, and updated the datatypes_conf.xml.
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
Thanks for any advice,
Cheers, Joachim
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/7105c53139d4b8649e6a3714...
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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Joachim Jacob | VIB |