I'm trying to install a custom tool "dataOverview.pl" into my local Galaxy instance. I followed the guidelines for creating the xml file "dataOverview.xml" and the tool_dependencies.xml file. For the tool_dependencies file, I used the Jupyter Notebook: http://nbviewer.jupyter.org/github/bgruening/notebooks/blob/master/Perl/perl_package_to_galaxy_tool_dependency.ipynb. The resulting tool_dependencies.xml file looks like this:
<tool_dependency> <package name="perl_bio_seqio" version="1.01"> <install version="1.0"> <actions> <action type="setup_perl_environment"> <repository name="package_perl_5_18" owner="iuc"> <package name="perl" version="5.18.1" /> </repository> </action> </actions> </install> <readme><![CDATA[ Perl package: Bio::SeqIO ]]> </readme> </package> </tool_dependency>
The input fields appear fine in Galaxy, but when I load the data and execute the tool, I get this error:
------------- EXCEPTION: Bio::Root::Exception ------------- MSG: EMBL stream with no ID. Not embl in my book STACK: Error::throw STACK: Bio::Root::Root::throw /Library/Perl/5.18/Bio/Root/Root.pm:449 STACK: Bio::SeqIO::embl::next_seq/Library/Perl/5.18/Bio/SeqIO/embl.pm:204 STACK: /Users/margaretantonio/galaxy/tools/myTools/dataOverview.pl:337
It appears to me that the required package BioSeqIO is not installed properly. I tried to follow online examples, but I suspect that I incorrectly designated the package in the <requirements> tag in dataOverview.xml.
<requirements> <requirement type="package" version="5.18.1">perl</requirement> </requirements>
Can someone help me see where I went wrong here? Also, I couldn't find any documentation/explanation on what the Jupyter Notebook mentioned above does/creates. So any input could help me troubleshoot. Note: I am also using the GetOpt::Long Perl module.