Trackster error: not able to find the chrom len file

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Trackster error: not able to find the chrom len file

Joachim Jacob
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


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Re: Trackster error: not able to find the chrom len file

Joachim Jacob
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
>

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Re: Trackster error: not able to find the chrom len file

Jeremy Goecks
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:


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:


Best,
J.

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