Question: Galaxy custom tool that uses perl module Bio::Seq::IO throws error
gravatar for margaretantonio
2.2 years ago by
margaretantonio0 wrote:

I'm trying to install a custom tool "" 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: The resulting tool_dependencies.xml file looks like this:

<package name="perl_bio_seqio" version="1.01">
        <install version="1.0">
                <action type="setup_perl_environment">
                    <repository name="package_perl_5_18" owner="iuc">
                        <package name="perl" version="5.18.1" />
            Perl package: Bio::SeqIO

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/ 
STACK: Bio::SeqIO::embl::next_seq/Library/Perl/5.18/Bio/SeqIO/ 
STACK: /Users/margaretantonio/galaxy/tools/myTools/

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.

        <requirement type="package" version="5.18.1">perl</requirement>

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.

perl perlmodule bioseqio galaxy • 672 views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by margaretantonio0
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