Hi Rui,

The Extract Genomic DNA Tool has not yet been updated to work with tool Data 
Tables. 

Additionally, this tool requires TwoBit formatted files when selecting from 
built-in data — when selecting a FASTA from your history, the fasta file is 
converted to TwoBit internally in the tool before extracting sequence chunks.

There is a TwoBit builder Data Manager under development 
(https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder),
 that hasn’t made it out to the ToolShed just yet, but it won’t be helpful 
until the  the Extract Genomic DNA Tool is updated: 
https://trello.com/c/8unnSp7H


Thanks for using Galaxy,

Dan


On Apr 7, 2015, at 12:16 AM, Beginner TI <ruiwang...@gmail.com> wrote:

> Hi All,
> 
> I just made a new local instance, installed the fetch_all_fasta data manager, 
> downloaded mm9 fasta. Then I noticed the following:
> 
> in tool_data_table_conf.xml, it has:
> 
>     <table name="all_fasta" comment_char="#">
>         <columns>value, dbkey, name, path</columns>
>         <file path="tool-data/all_fasta.loc" />
>     </table>
> 
> however in shed_tool_data_table_conf.xml, it has:
> 
> <table comment_char="#" name="all_fasta">
>         <columns>value, dbkey, name, path</columns>
>         <file 
> path="/auto/rcf-proj/yc1/galaxy-suite/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/cca219f2b212/all_fasta.loc"
>  />
>     
> <tool_shed_repository><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_fetch_genome_all_fasta</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>cca219f2b212</installed_changeset_revision></tool_shed_repository></table>
> 
> in tool-data, all_fasta.loc is empty, but in the all_fasta.loc of the 
> shed_tool entry, it shows:
> 
> mm9     mm9     Mouse July 2007 (NCBI37/mm9) (mm9)      
> /auto/rcf-proj/yc1/galaxy-suite/galaxy-dist/tool-data/mm9/seq/mm9.fa
> 
> So if I try "Extract Genomic DNA function", I could see the parameter passed 
> to the command line is 
> 
> -g "/auto/rcf-proj/yc1/galaxy-suite/galaxy-dist/tool-data" 
> 
> which does not host the data. It should be at least
> 
> -g "/auto/rcf-proj/yc1/galaxy-suite/galaxy-dist/tool-data/mm9/seq"
> 
> I thought that data manager will automatically populate these loc files? Am I 
> missing something obvious?  I could manually modify tool_data_table_conf.xml 
> to let it point to
> 
> /auto/rcf-proj/yc1/galaxy-suite/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/cca219f2b212/all_fasta.loc
> 
> This would work, but it is ugly. Could someone please give me a hand to fix 
> this?
> 
> Thanks,
> Rui
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