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.