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/dat...), 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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