[ensembl-dev] Bulk download of Microarray Probe mapping via MySQL

Alex Holman aholman at jimmy.harvard.edu
Thu Jul 18 18:49:42 BST 2013


Hi Nathan, 
Thanks a lot for writing this, its a big help. I'm having a couple of problems getting it going.

I'm on v.72 of the api, and my command line for running the script is:
perl ../ensembl_scripts/dump_array_annotations.pl -user anonymous -pass -port 3306 -host useastdb.ensembl.org -dbname "homo_sapiens_funcgen_72_37" -arrays HuGene-1_0-st-v1 -features

First, a simple issue that I solved on my own, but I'm going to just list here for posterity.  
The script looks for a module DBAdaptor.pm located in the ensembl-hive directory of the CVS.
Can't locate Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm
ensembl-hive doesn't appear to come down with the standard CVS commands listed in the ensembl CVS instructions: http://useast.ensembl.org/info/docs/api/api_cvs.html as it doesn't appear to be associated with branch 72.  If you remove '-r branch-ensembl-72' from the CVS command, ensembl-hive downloads properly.  

Second, something that I haven't solved yet.
When I try to run the script with the above command I get the error:
Can't use an undefined value as a HASH reference at /Users/alex/Work/2013_07_01_get_Ensembl_annotations/ensembl_api/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/Utils/DBAdaptorHelper.pm line 282.

Line 282 in that module is the %{$core_params} hash reference used in calling create_DBAdaptor_from_params.

sub create_Funcgen_DBAdaptor_from_options {
  my $db_opts = $_[0];
  
  my $funcgen_params = ${&process_DB_options($db_opts, ['funcgen'])}{funcgen};
  #This simply allows dnadb_params to be optional
  my $core_params    = ${&process_DB_options($db_opts, ['core'], 1, 'dnadb')}{core};
  
  return create_DBAdaptor_from_params({%{$funcgen_params},
**line 282**                           %{$core_params}},
                                      'funcgen');  
}

In addition, I tried using the virtual machine image provided from Ensembl just to verify that the issue wasn't something with my install.  After dealing with the ensemble-hive issue above I ran into the same problem.
http://useast.ensembl.org/info/data/virtual_machine.html

Thanks again for working on this.
-Alex-
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