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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