Problem with Data Manager "Create DBKey and Reference Genome"

Question: Problem with Data Manager "Create DBKey and Reference Genome"

3.4 years ago by

France

Hi everyone,

I had a bug when I tried to use the data manager "Create DBKey and Reference Genome". I simply wanted to add hg38 genome. Apparently, when I filled the information, I have to set information with no space.

Here is the error when I write "Human Dec. 2013 (GRCh38/hg38)(hg38)" as "Name of sequence"

IOError: [Errno 2] No such file or directory: u'/home/galaxy/galaxy_14avr2015/galaxy/database/job_working_directory/000/50/dataset_108_files/Human Dec. 2013 (GRCh38/hg38)(hg38).fa'

And here is the error when I write "Human Dec. 2013 (GRCh38/hg38)(hg38)" as "dbkey"

IOError: [Errno 2] No such file or directory: u'/home/galaxy/galaxy_14avr2015/galaxy/database/job_working_directory/000/51/dataset_109_files/Human Dec. 2013 (GRCh38/hg38)(hg38).len'

When I replaced "Human Dec. 2013 (GRCh38/hg38)(hg38)" with "hg38" the data manager worked well.

Could it be possible to correct this behaviour ?

Thank you,

Christophe

bug data manager • 1.4k views

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modified 3.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by christophe.habib • 340

3.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

A "dbkey" is a single word identifier for a specific genome version. Each are unique and consistent of alphanumeric characters plus (optionally) underscores. This is the value that appears in the user interface as the "database" attribute. When a remote genome is fetched, this should exactly match the genome identifier used by the target data source.

The description of the genome is permitted to contain other characters (the variation can be seen in the existing list of reference genomes - aka the "builds.txt" list) on the Main Galaxy instance in a few places, including: 1) Upload tool 2) On the first tab of the "Edit Attributes" form (found by clicking on the upper right pencil icon for any existing dataset).

We'll double check that description (vs dbkey) is working correctly with this Data Manager and get back to you if there is an issue with expected functionality.

Thanks for reporting the usage issue and hopefully this helps, Jen, Galaxy team

ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

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