Problem configuring local galaxy central installs and GATK beta pipeline
Hi, I noted there have been a change on the way GATK tools read picard_index.loc, from "tool_data_table_conf.xml": <!-- Location of Picard dict files valid for GATK --> <table name="gatk_picard_indexes" comment_char="#"> <columns>value, dbkey, name, path, tools_valid_for</columns> <file path="tool-data/picard_index.loc" /> </table> And I can't decipher how to use column "tools_valid_for". I was able to show selectable reference genomes in one of the tools by adding its id there, but I don't know how to add the rest. Should I separate them by spaces? commas? tabs?, none of these seem to work for me. Also, what is the best way to identify a tool id, should I just use file name for its xml file? Thanks in advance, Carlos
Hi Carlos, For now, put 'gatk' in that column for the builds that you want to make available. At this point it is not actually checking the contents, but the presence of the additional column is enough to allow it to be used in the GATK in Galaxy. In the future the behavior will be properly enhanced to work properly on a comma separated listing. Thanks for using Galaxy, Dan On Nov 15, 2011, at 12:14 PM, Carlos Borroto wrote:
Hi,
I noted there have been a change on the way GATK tools read picard_index.loc, from "tool_data_table_conf.xml": <!-- Location of Picard dict files valid for GATK --> <table name="gatk_picard_indexes" comment_char="#"> <columns>value, dbkey, name, path, tools_valid_for</columns> <file path="tool-data/picard_index.loc" /> </table>
And I can't decipher how to use column "tools_valid_for". I was able to show selectable reference genomes in one of the tools by adding its id there, but I don't know how to add the rest. Should I separate them by spaces? commas? tabs?, none of these seem to work for me.
Also, what is the best way to identify a tool id, should I just use file name for its xml file?
Thanks in advance, Carlos ___________________________________________________________ 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:
Hi Dan, thanks for your help. I also just realized some of the tools won't show a reference genome option if the selected input is not associated with an available reference, in the case the input it is associated, that genome is automatically selected. Which made me think, why put "Using reference genome:" as a drop down menu or as an option at all for these tools? I feel it will only confuse the user. I do realize this is a very early stage of support for these tools and I'm very grateful you are helping me testing them at this time. Thanks, Carlos On Tue, Nov 15, 2011 at 3:38 PM, Daniel Blankenberg <dan@bx.psu.edu> wrote:
Hi Carlos,
For now, put 'gatk' in that column for the builds that you want to make available. At this point it is not actually checking the contents, but the presence of the additional column is enough to allow it to be used in the GATK in Galaxy. In the future the behavior will be properly enhanced to work properly on a comma separated listing.
Thanks for using Galaxy,
Dan
On Nov 15, 2011, at 12:14 PM, Carlos Borroto wrote:
Hi,
I noted there have been a change on the way GATK tools read picard_index.loc, from "tool_data_table_conf.xml": <!-- Location of Picard dict files valid for GATK --> <table name="gatk_picard_indexes" comment_char="#"> <columns>value, dbkey, name, path, tools_valid_for</columns> <file path="tool-data/picard_index.loc" /> </table>
And I can't decipher how to use column "tools_valid_for". I was able to show selectable reference genomes in one of the tools by adding its id there, but I don't know how to add the rest. Should I separate them by spaces? commas? tabs?, none of these seem to work for me.
Also, what is the best way to identify a tool id, should I just use file name for its xml file?
Thanks in advance, Carlos ___________________________________________________________ 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:
participants (2)
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Carlos Borroto -
Daniel Blankenberg