[biomart-users] Please help with installation of Ensembl Biomart Perl API

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[biomart-users] Please help with installation of Ensembl Biomart Perl API

Tatyana Livshultz
Hello:

I have installed the Ensembl BioMart Perl API on a Linux machine following the instructions at this website.

When I run the example query included in the installation:

~/biomart-perl/scripts$ perl  apiExample_1.pl

I get the following error message:

Cached Registry Unavailable...

Running Complete Clean...



 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE central_registry.CHECK YOUR SETTINGS
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Can't call method "getRegistryXML" on an undefined value at /home/REDACTED/biomart-perl/lib/BioMart/Initializer.pm line 855.

The contents of line 855 in /biomart-perl/lib/BioMart/Initializer.pm are as follows.
my $regXML = $pointer->getRegistryXML();

The contents of the "biomart-perl/conf/martURLLocation.xml" file have been updated following the instructions on the website to the following:


<MartRegistry>
  <MartURLLocation database="ensembl_mart_100" default="1" displayName="Ensembl Genes 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_100" default="" displayName="Mouse strains 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_100" default="" displayName="Sequence" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_100" default="" displayName="Ontology" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_100" default="" displayName="Genomic features 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_100" default="" displayName="Ensembl Variation 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_100" default="" displayName="Ensembl Regulation 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>




I would really be grateful for any assistance here.
Thank you,
Tanya


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Re: [biomart-users] Please help with installation of Ensembl Biomart Perl API

Syed Haider-5
Hi Tanya,

Ensembl BioMart seems to be down at the moment. You may want to point your registry to this (archived) installation:


Hope this helps,
Syed




On Tue, 12 May 2020 at 17:01, Tatyana Livshultz <[hidden email]> wrote:
Hello:

I have installed the Ensembl BioMart Perl API on a Linux machine following the instructions at this website.

When I run the example query included in the installation:

~/biomart-perl/scripts$ perl  apiExample_1.pl

I get the following error message:

Cached Registry Unavailable...

Running Complete Clean...



 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE central_registry.CHECK YOUR SETTINGS
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Can't call method "getRegistryXML" on an undefined value at /home/REDACTED/biomart-perl/lib/BioMart/Initializer.pm line 855.

The contents of line 855 in /biomart-perl/lib/BioMart/Initializer.pm are as follows.
my $regXML = $pointer->getRegistryXML();

The contents of the "biomart-perl/conf/martURLLocation.xml" file have been updated following the instructions on the website to the following:


<MartRegistry>
  <MartURLLocation database="ensembl_mart_100" default="1" displayName="Ensembl Genes 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_100" default="" displayName="Mouse strains 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_100" default="" displayName="Sequence" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_100" default="" displayName="Ontology" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_100" default="" displayName="Genomic features 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_100" default="" displayName="Ensembl Variation 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_100" default="" displayName="Ensembl Regulation 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>




I would really be grateful for any assistance here.
Thank you,
Tanya


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Re: [biomart-users] Please help with installation of Ensembl Biomart Perl API

Tatyana Livshultz
Dear Syed:

Thank you for your quick response. I've edited the contents of the  "biomart-perl/conf/martURLLocation.xml" file to
<MartRegistry>
  <MartURLLocation database="ensembl_mart_99" default="1" displayName="Ensembl Genes 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_99" default="" displayName="Mouse strains 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_99" default="" displayName="Sequence" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_99" default="" displayName="Ontology" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_99" default="" displayName="Genomic features 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_99" default="" displayName="Ensembl Variation 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_99" default="" displayName="Ensembl Regulation 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>

but I get the exact same error message. Any other ideas? Thank you. Tanya

Cached Registry Unavailable...

Running Complete Clean...



 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE central_registry.CHECK YOUR SETTINGS
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Can't call method "getRegistryXML" on an undefined value at /home/REDACTED/biomart-perl/lib/BioMart/Initializer.pm line 855.

On Tuesday, May 12, 2020 at 11:07:43 AM UTC-5, Syed Haider wrote:
Hi Tanya,

Ensembl BioMart seems to be down at the moment. You may want to point your registry to this (archived) installation:

<a href="http://jan2020.archive.ensembl.org/biomart/martservice?type=registry" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHH3wDrtqfWDu0qpyAwnV7I277QOg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHH3wDrtqfWDu0qpyAwnV7I277QOg&#39;;return true;">http://jan2020.archive.ensembl.org/biomart/martservice?type=registry

Hope this helps,
Syed




On Tue, 12 May 2020 at 17:01, Tatyana Livshultz <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="Wa20kyhcBQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">tatyanal...@...> wrote:
Hello:

I have installed the Ensembl BioMart Perl API on a Linux machine following the instructions at this website.
<a href="http://useast.ensembl.org/info/data/biomart/biomart_perl_api.html" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org%2Finfo%2Fdata%2Fbiomart%2Fbiomart_perl_api.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH9vWauvyOgVKFdUlJT-DXfPpRhtg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org%2Finfo%2Fdata%2Fbiomart%2Fbiomart_perl_api.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH9vWauvyOgVKFdUlJT-DXfPpRhtg&#39;;return true;">http://useast.ensembl.org/info/data/biomart/biomart_perl_api.html

When I run the example query included in the installation:

~/biomart-perl/scripts$ perl  apiExample_1.pl

I get the following error message:

Cached Registry Unavailable...

Running Complete Clean...



 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE central_registry.CHECK YOUR SETTINGS
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Can't call method "getRegistryXML" on an undefined value at /home/REDACTED/biomart-perl/lib/BioMart/Initializer.pm line 855.

The contents of line 855 in /biomart-perl/lib/BioMart/Initializer.pm are as follows.
my $regXML = $pointer->getRegistryXML();

The contents of the "biomart-perl/conf/martURLLocation.xml" file have been updated following the instructions on the website to the following:
<a href="http://useast.ensembl.org/biomart/martservice?type=registry" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF4BURgD_4gWEb6xn7FHeAxuVc_WQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF4BURgD_4gWEb6xn7FHeAxuVc_WQ&#39;;return true;">http://useast.ensembl.org/biomart/martservice?type=registry


<MartRegistry>
  <MartURLLocation database="ensembl_mart_100" default="1" displayName="Ensembl Genes 100" host="<a href="http://www.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_100" default="" displayName="Mouse strains 100" host="<a href="http://www.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_100" default="" displayName="Sequence" host="<a href="http://www.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_100" default="" displayName="Ontology" host="<a href="http://www.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_100" default="" displayName="Genomic features 100" host="<a href="http://www.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_100" default="" displayName="Ensembl Variation 100" host="<a href="http://www.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_100" default="" displayName="Ensembl Regulation 100" host="<a href="http://www.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>




I would really be grateful for any assistance here.
Thank you,
Tanya


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Re: [biomart-users] Please help with installation of Ensembl Biomart Perl API

Tatyana Livshultz
I note that the folder biomart-perl/conf has additional xml files, beside martURLLocation.xml, that have the "MartRegistry" markup. Do any of them need to be changed? Thank you. Tanya

registryURLPointer.xml
registry_DOM_XML
registryDBPointer.xml
projectRegistry.xml
martDBLocation.xml



On Tuesday, May 12, 2020 at 11:38:44 AM UTC-5, Tatyana Livshultz wrote:
Dear Syed:

Thank you for your quick response. I've edited the contents of the  "biomart-perl/conf/martURLLocation.xml" file to
<a href="http://jan2020.archive.ensembl.org/biomart/martservice?type=registry" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHH3wDrtqfWDu0qpyAwnV7I277QOg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHH3wDrtqfWDu0qpyAwnV7I277QOg&#39;;return true;">http://jan2020.archive.ensembl.org/biomart/martservice?type=registry
<MartRegistry>
  <MartURLLocation database="ensembl_mart_99" default="1" displayName="Ensembl Genes 99" host="<a href="http://jan2020.archive.ensembl.org/" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;">jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_99" default="" displayName="Mouse strains 99" host="<a href="http://jan2020.archive.ensembl.org/" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;">jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_99" default="" displayName="Sequence" host="<a href="http://jan2020.archive.ensembl.org/" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;">jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_99" default="" displayName="Ontology" host="<a href="http://jan2020.archive.ensembl.org/" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;">jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_99" default="" displayName="Genomic features 99" host="<a href="http://jan2020.archive.ensembl.org/" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;">jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_99" default="" displayName="Ensembl Variation 99" host="<a href="http://jan2020.archive.ensembl.org/" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;">jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_99" default="" displayName="Ensembl Regulation 99" host="<a href="http://jan2020.archive.ensembl.org/" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFKsOma31Y79hPsdDSIwvenEQk7-A&#39;;return true;">jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>

but I get the exact same error message. Any other ideas? Thank you. Tanya

Cached Registry Unavailable...

Running Complete Clean...



 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE central_registry.CHECK YOUR SETTINGS
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Can't call method "getRegistryXML" on an undefined value at /home/REDACTED/biomart-perl/lib/BioMart/Initializer.pm line 855.

On Tuesday, May 12, 2020 at 11:07:43 AM UTC-5, Syed Haider wrote:
Hi Tanya,

Ensembl BioMart seems to be down at the moment. You may want to point your registry to this (archived) installation:

<a href="http://jan2020.archive.ensembl.org/biomart/martservice?type=registry" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHH3wDrtqfWDu0qpyAwnV7I277QOg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fjan2020.archive.ensembl.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHH3wDrtqfWDu0qpyAwnV7I277QOg&#39;;return true;">http://jan2020.archive.ensembl.org/biomart/martservice?type=registry

Hope this helps,
Syed




On Tue, 12 May 2020 at 17:01, Tatyana Livshultz <[hidden email]> wrote:
Hello:

I have installed the Ensembl BioMart Perl API on a Linux machine following the instructions at this website.
<a href="http://useast.ensembl.org/info/data/biomart/biomart_perl_api.html" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org%2Finfo%2Fdata%2Fbiomart%2Fbiomart_perl_api.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH9vWauvyOgVKFdUlJT-DXfPpRhtg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org%2Finfo%2Fdata%2Fbiomart%2Fbiomart_perl_api.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH9vWauvyOgVKFdUlJT-DXfPpRhtg&#39;;return true;">http://useast.ensembl.org/info/data/biomart/biomart_perl_api.html

When I run the example query included in the installation:

~/biomart-perl/scripts$ perl  apiExample_1.pl

I get the following error message:

Cached Registry Unavailable...

Running Complete Clean...



 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE central_registry.CHECK YOUR SETTINGS
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Can't call method "getRegistryXML" on an undefined value at /home/REDACTED/biomart-perl/lib/BioMart/Initializer.pm line 855.

The contents of line 855 in /biomart-perl/lib/BioMart/Initializer.pm are as follows.
my $regXML = $pointer->getRegistryXML();

The contents of the "biomart-perl/conf/martURLLocation.xml" file have been updated following the instructions on the website to the following:
<a href="http://useast.ensembl.org/biomart/martservice?type=registry" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF4BURgD_4gWEb6xn7FHeAxuVc_WQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org%2Fbiomart%2Fmartservice%3Ftype%3Dregistry\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF4BURgD_4gWEb6xn7FHeAxuVc_WQ&#39;;return true;">http://useast.ensembl.org/biomart/martservice?type=registry


<MartRegistry>
  <MartURLLocation database="ensembl_mart_100" default="1" displayName="Ensembl Genes 100" host="<a href="http://www.ensembl.org" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_100" default="" displayName="Mouse strains 100" host="<a href="http://www.ensembl.org" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_100" default="" displayName="Sequence" host="<a href="http://www.ensembl.org" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_100" default="" displayName="Ontology" host="<a href="http://www.ensembl.org" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_100" default="" displayName="Genomic features 100" host="<a href="http://www.ensembl.org" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_100" default="" displayName="Ensembl Variation 100" host="<a href="http://www.ensembl.org" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_100" default="" displayName="Ensembl Regulation 100" host="<a href="http://www.ensembl.org" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>




I would really be grateful for any assistance here.
Thank you,
Tanya


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Re: [biomart-users] Please help with installation of Ensembl Biomart Perl API

Syed Haider-5
In reply to this post by Tatyana Livshultz
Hi Tanya,

Not directly answering your question but offering a different solution: have you tried the REST webservice request i.e XML query. You can see its template by hitting the XML button on MartView. That will by-pass the biomart-perl API and you can send the query from any programming language. See section 6.6 here:


Best,
Syed





On Tue, 12 May 2020 at 17:38, Tatyana Livshultz <[hidden email]> wrote:
Dear Syed:

Thank you for your quick response. I've edited the contents of the  "biomart-perl/conf/martURLLocation.xml" file to
<MartRegistry>
  <MartURLLocation database="ensembl_mart_99" default="1" displayName="Ensembl Genes 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_99" default="" displayName="Mouse strains 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_99" default="" displayName="Sequence" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_99" default="" displayName="Ontology" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_99" default="" displayName="Genomic features 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_99" default="" displayName="Ensembl Variation 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_99" default="" displayName="Ensembl Regulation 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>

but I get the exact same error message. Any other ideas? Thank you. Tanya

Cached Registry Unavailable...

Running Complete Clean...



 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE central_registry.CHECK YOUR SETTINGS
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Can't call method "getRegistryXML" on an undefined value at /home/REDACTED/biomart-perl/lib/BioMart/Initializer.pm line 855.

On Tuesday, May 12, 2020 at 11:07:43 AM UTC-5, Syed Haider wrote:
Hi Tanya,

Ensembl BioMart seems to be down at the moment. You may want to point your registry to this (archived) installation:


Hope this helps,
Syed




On Tue, 12 May 2020 at 17:01, Tatyana Livshultz <[hidden email]> wrote:
Hello:

I have installed the Ensembl BioMart Perl API on a Linux machine following the instructions at this website.

When I run the example query included in the installation:

~/biomart-perl/scripts$ perl  apiExample_1.pl

I get the following error message:

Cached Registry Unavailable...

Running Complete Clean...



 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE central_registry.CHECK YOUR SETTINGS
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Can't call method "getRegistryXML" on an undefined value at /home/REDACTED/biomart-perl/lib/BioMart/Initializer.pm line 855.

The contents of line 855 in /biomart-perl/lib/BioMart/Initializer.pm are as follows.
my $regXML = $pointer->getRegistryXML();

The contents of the "biomart-perl/conf/martURLLocation.xml" file have been updated following the instructions on the website to the following:


<MartRegistry>
  <MartURLLocation database="ensembl_mart_100" default="1" displayName="Ensembl Genes 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_100" default="" displayName="Mouse strains 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_100" default="" displayName="Sequence" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_100" default="" displayName="Ontology" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_100" default="" displayName="Genomic features 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_100" default="" displayName="Ensembl Variation 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_100" default="" displayName="Ensembl Regulation 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>




I would really be grateful for any assistance here.
Thank you,
Tanya


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Re: [biomart-users] Please help with installation of Ensembl Biomart Perl API

Tatyana Livshultz
Hi Syed:

Thank you for the tip. I was able to query plants.ensembl.org using the unix wget command and the XML query obtained from MartView. I got useful additional information here:


I want to construct a query to loop through all the plant genomes in Ensembl and download all the DNA sequences of one protein family. Do you (or anyone else in this group) have a wget script that does something similar with a loop that I can look at and modify? Also, how can I get a list of all the names of the plant datasets in Ensembl? The published list of genomes, https://plants.ensembl.org/species.html, doesn't give the actual dataset names used in the BioMart query.

Thank you for your help. Best regards, Tanya


On Tue, May 12, 2020 at 2:21 PM Syed Haider <[hidden email]> wrote:
Hi Tanya,

Not directly answering your question but offering a different solution: have you tried the REST webservice request i.e XML query. You can see its template by hitting the XML button on MartView. That will by-pass the biomart-perl API and you can send the query from any programming language. See section 6.6 here:


Best,
Syed





On Tue, 12 May 2020 at 17:38, Tatyana Livshultz <[hidden email]> wrote:
Dear Syed:

Thank you for your quick response. I've edited the contents of the  "biomart-perl/conf/martURLLocation.xml" file to
<MartRegistry>
  <MartURLLocation database="ensembl_mart_99" default="1" displayName="Ensembl Genes 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_99" default="" displayName="Mouse strains 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_99" default="" displayName="Sequence" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_99" default="" displayName="Ontology" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_99" default="" displayName="Genomic features 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_99" default="" displayName="Ensembl Variation 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_99" default="" displayName="Ensembl Regulation 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>

but I get the exact same error message. Any other ideas? Thank you. Tanya

Cached Registry Unavailable...

Running Complete Clean...



 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE central_registry.CHECK YOUR SETTINGS
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Can't call method "getRegistryXML" on an undefined value at /home/REDACTED/biomart-perl/lib/BioMart/Initializer.pm line 855.

On Tuesday, May 12, 2020 at 11:07:43 AM UTC-5, Syed Haider wrote:
Hi Tanya,

Ensembl BioMart seems to be down at the moment. You may want to point your registry to this (archived) installation:


Hope this helps,
Syed




On Tue, 12 May 2020 at 17:01, Tatyana Livshultz <[hidden email]> wrote:
Hello:

I have installed the Ensembl BioMart Perl API on a Linux machine following the instructions at this website.

When I run the example query included in the installation:

~/biomart-perl/scripts$ perl  apiExample_1.pl

I get the following error message:

Cached Registry Unavailable...

Running Complete Clean...



 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE central_registry.CHECK YOUR SETTINGS
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Can't call method "getRegistryXML" on an undefined value at /home/REDACTED/biomart-perl/lib/BioMart/Initializer.pm line 855.

The contents of line 855 in /biomart-perl/lib/BioMart/Initializer.pm are as follows.
my $regXML = $pointer->getRegistryXML();

The contents of the "biomart-perl/conf/martURLLocation.xml" file have been updated following the instructions on the website to the following:


<MartRegistry>
  <MartURLLocation database="ensembl_mart_100" default="1" displayName="Ensembl Genes 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_100" default="" displayName="Mouse strains 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_100" default="" displayName="Sequence" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_100" default="" displayName="Ontology" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_100" default="" displayName="Genomic features 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_100" default="" displayName="Ensembl Variation 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_100" default="" displayName="Ensembl Regulation 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>




I would really be grateful for any assistance here.
Thank you,
Tanya


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Re: [biomart-users] Please help with installation of Ensembl Biomart Perl API

Syed Haider-5
Hi Tanya,

You can retrieve dataset names programmatically through BioMart webservice, see documentation section 6.6 in the docs in my last email. For your question on getting dataset names, you need this:


which in essence is constructed by first running the type=registry and using the info returned by the registry request, you can construct the above command.

HTH,
Syed




On Wed, 13 May 2020 at 03:08, Tatyana Livshultz <[hidden email]> wrote:
Hi Syed:

Thank you for the tip. I was able to query plants.ensembl.org using the unix wget command and the XML query obtained from MartView. I got useful additional information here:


I want to construct a query to loop through all the plant genomes in Ensembl and download all the DNA sequences of one protein family. Do you (or anyone else in this group) have a wget script that does something similar with a loop that I can look at and modify? Also, how can I get a list of all the names of the plant datasets in Ensembl? The published list of genomes, https://plants.ensembl.org/species.html, doesn't give the actual dataset names used in the BioMart query.

Thank you for your help. Best regards, Tanya


On Tue, May 12, 2020 at 2:21 PM Syed Haider <[hidden email]> wrote:
Hi Tanya,

Not directly answering your question but offering a different solution: have you tried the REST webservice request i.e XML query. You can see its template by hitting the XML button on MartView. That will by-pass the biomart-perl API and you can send the query from any programming language. See section 6.6 here:


Best,
Syed





On Tue, 12 May 2020 at 17:38, Tatyana Livshultz <[hidden email]> wrote:
Dear Syed:

Thank you for your quick response. I've edited the contents of the  "biomart-perl/conf/martURLLocation.xml" file to
<MartRegistry>
  <MartURLLocation database="ensembl_mart_99" default="1" displayName="Ensembl Genes 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_99" default="" displayName="Mouse strains 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_99" default="" displayName="Sequence" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_99" default="" displayName="Ontology" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_99" default="" displayName="Genomic features 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_99" default="" displayName="Ensembl Variation 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_99" default="" displayName="Ensembl Regulation 99" host="jan2020.archive.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>

but I get the exact same error message. Any other ideas? Thank you. Tanya

Cached Registry Unavailable...

Running Complete Clean...



 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE central_registry.CHECK YOUR SETTINGS
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Can't call method "getRegistryXML" on an undefined value at /home/REDACTED/biomart-perl/lib/BioMart/Initializer.pm line 855.

On Tuesday, May 12, 2020 at 11:07:43 AM UTC-5, Syed Haider wrote:
Hi Tanya,

Ensembl BioMart seems to be down at the moment. You may want to point your registry to this (archived) installation:


Hope this helps,
Syed




On Tue, 12 May 2020 at 17:01, Tatyana Livshultz <[hidden email]> wrote:
Hello:

I have installed the Ensembl BioMart Perl API on a Linux machine following the instructions at this website.

When I run the example query included in the installation:

~/biomart-perl/scripts$ perl  apiExample_1.pl

I get the following error message:

Cached Registry Unavailable...

Running Complete Clean...



 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
                
 COULD NOT CONNECT TO DATABASE central_registry.CHECK YOUR SETTINGS
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Can't call method "getRegistryXML" on an undefined value at /home/REDACTED/biomart-perl/lib/BioMart/Initializer.pm line 855.

The contents of line 855 in /biomart-perl/lib/BioMart/Initializer.pm are as follows.
my $regXML = $pointer->getRegistryXML();

The contents of the "biomart-perl/conf/martURLLocation.xml" file have been updated following the instructions on the website to the following:


<MartRegistry>
  <MartURLLocation database="ensembl_mart_100" default="1" displayName="Ensembl Genes 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="mouse_mart_100" default="" displayName="Mouse strains 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_100" default="" displayName="Sequence" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_100" default="" displayName="Ontology" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_100" default="" displayName="Genomic features 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_100" default="" displayName="Ensembl Variation 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_100" default="" displayName="Ensembl Regulation 100" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>




I would really be grateful for any assistance here.
Thank you,
Tanya


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