From: Eric Rasche <esr@tamu.edu>
Sent: Thursday, January 28, 2016 4:40 PM
To: Wang, Xiaofei; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] 'bp_genbank2gff3' installation error and running error

Hi Xiaofei,

I don't believe I saw a response to your message. I'm the author of the Galaxy wrapper for bp_genbank2gff3, but my ability to help here is somewhat limited.

Dear there,

I'd like to convert genebank flat file to GFF. So, I am trying to install this tool shed  to my local galaxy. But I got an error as below.

Does it associated with dependencies? I see it needs these ​ . How can I check if I have all these?

You can check which dependencies are currently installed by going to your Galaxy server's Admin page, and clicking on "Manage Installed Tools". Galaxy won't re-install things if they're already installed.

​

This error I'm afraid I do not know how to help with. My best suggestion is "make sure you're on a recent version of Galaxy".

Also, I see there is the same tool in this website https://galaxy.cbio.mskcc.org/root?tool_id=fml_gbk2gff (see below). It should be also galaxy but I need to register an account for it. Do you know what is the relationship between this website and the galaxy?

They are a website which has deployed Galaxy for public use, not the same as "Main" at usegalaxy.org, or your private Galaxy.

BTW, I received an error when I used the tool on this website. I think if they are same tool, the galaxy team should know the reason for it. Here is the error as below.

This is not the same tool, they have a "gbk_to_gff.py" script which I am not aware of, while my bp_genbank2gff wrapper wraps the official bioperl genbank2gff3 converter that ships with bioperl.

GFF Toolkit (v0.1)

GROOMING PROGRAMS

Examine_GFF file Parent-Child relations

FeatureScan gives an overview about GFF feature content

CONVERTER PROGRAMS

GTF_to_GFF3 converter

BED_to_GFF3 converter

GFF3_to_BED converter

GBK-to-GFF converter

​

Thanks!

Best,

Xiaofei

Apologies for the lack of help Xiaofei. Good luck getting it all to work.

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Ciao,
Eric

-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
esr@tamu.edu