Question: No options available in "ANNOVAR annotate VCF" by devteam
1
gravatar for christophe.habib
3.1 years ago by
France
christophe.habib340 wrote:

Hello everyone,

I am trying to configure ANNOVAR (the one by the Devteam) in galaxy to set the databases available for annotation. Here is what I made already :

  • In the tool_data_table_conf.xml file I wrote the file path of annovar_index.loc.
  • In the tool_dependencies.xml file I wrote the path of the folder containing annovar scripts
  • And in annovar_index.loc I wrote just to test : "exac03    hg38    filter   path_to_humandb"

On note, I also tried to give the full path to the .idx file corresponding to exac03 for hg38.

Unfortunately, when I reboot galaxy I still have "No options available" and I can't select exac03 as mentionned before.

I am pretty sure I miss something really important. Do I have to modify the wrapper to make these databases options available? What am I supposed to do to see the databases availables in the form.

Thank you for your help.

 

 

devteam configuration annovar • 1.0k views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by christophe.habib340
0
gravatar for christophe.habib
3.1 years ago by
France
christophe.habib340 wrote:

Does anyone tried to use this tool? The wrapper is from the dev team!
 

ADD COMMENTlink written 3.1 years ago by christophe.habib340
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