​Hi,


Thanks for your reply! I thought my question is flood in high volume of threads :)


It might be the old version of local galaxy that I used. Anyway, I figured it out by using " bp_genbank2gff3.pl" in BioPerl.​ 


Hope my experience can help the people who have some problem as mine.


Best,


Xiaofei

 



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.

On 12/30/2015 04:12 PM, Wang, Xiaofei wrote:

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.


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
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Texas A&M University
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