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.sz@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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