<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Nathan, <div>Thanks a lot for writing this, its a big help. I'm having a couple of problems getting it going.</div><div><br></div><div>I'm on v.72 of the api, and my command line for running the script is:</div><div>perl ../ensembl_scripts/dump_array_annotations.pl -user anonymous -pass -port 3306 -host <a href="http://useastdb.ensembl.org">useastdb.ensembl.org</a> -dbname "homo_sapiens_funcgen_72_37" -arrays HuGene-1_0-st-v1 -features</div><div><br></div><div>First, a simple issue that I solved on my own, but I'm going to just list here for posterity. </div><div>The script looks for a module DBAdaptor.pm located in the ensembl-hive directory of the CVS.</div><div>Can't locate Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm</div><div style="text-align: left;">ensembl-hive doesn't appear to come down with the standard CVS commands listed in the ensembl CVS instructions: <a href="http://useast.ensembl.org/info/docs/api/api_cvs.html">http://useast.ensembl.org/info/docs/api/api_cvs.html</a> as it doesn't appear to be associated with branch 72. If you remove '<span style="background-color: rgb(255, 255, 255); text-align: left; "><font color="#555555" face="Courier New, Courier, monospace"><span style="font-size: 13px; line-height: 16px;">-r branch-ensembl-72' from the CVS command, ensembl-hive downloads properly. </span></font></span></div><div style="text-align: left;"><span style="background-color: rgb(255, 255, 255); text-align: left; "><font color="#555555" face="Courier New, Courier, monospace"><span style="font-size: 13px; line-height: 16px;"><br></span></font></span></div><div style="text-align: left;"><span style="background-color: rgb(255, 255, 255); text-align: left; "><font color="#555555" face="Courier New, Courier, monospace"><span style="font-size: 13px; line-height: 16px;">Second, something that I haven't solved yet.</span></font></span></div><div style="text-align: left;"><span style="background-color: rgb(255, 255, 255); text-align: left; "><font color="#555555" face="Courier New, Courier, monospace"><span style="font-size: 13px; line-height: 16px;">When I try to run the script with the above command I get the error:</span></font></span></div><div style="text-align: left;">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.</div><div style="text-align: left;"><br></div><div style="text-align: left;">Line 282 in that module is the %{$core_params} hash reference used in calling create_DBAdaptor_from_params.</div><div style="text-align: left;"><br></div><div style="text-align: left;"><div>sub create_Funcgen_DBAdaptor_from_options {</div><div> my $db_opts = $_[0];</div><div> </div><div> my $funcgen_params = ${&process_DB_options($db_opts, ['funcgen'])}{funcgen};</div><div> #This simply allows dnadb_params to be optional</div><div> my $core_params = ${&process_DB_options($db_opts, ['core'], 1, 'dnadb')}{core};</div><div> </div><div> return create_DBAdaptor_from_params({%{$funcgen_params},</div><div>**line 282** %{$core_params}},</div><div> 'funcgen'); </div><div>}</div><div><br></div><div>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.</div><div><a href="http://useast.ensembl.org/info/data/virtual_machine.html">http://useast.ensembl.org/info/data/virtual_machine.html</a></div><div><br></div><div>Thanks again for working on this.</div><div>-Alex-</div></div></body></html>