?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 [cid:part1.05020703.02050004@tamu.edu] to my local galaxy. But I got an error as below.

Does it associated with dependencies? I see it needs these ? [cid:part2.08070605.08000804@tamu.edu] . 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.

?[cid:part3.09010306.04030504@tamu.edu]

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 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_GFFhttps://galaxy.cbio.mskcc.org/tool_runner?tool_id=gff_examine file Parent-Child relations FeatureScanhttps://galaxy.cbio.mskcc.org/tool_runner?tool_id=gff_available_limits gives an overview about GFF feature content CONVERTER PROGRAMS GTF_to_GFF3https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gtf2gff3 converter BED_to_GFF3https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_bed2gff converter GFF3_to_BEDhttps://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gff2bed converter GBK-to-GFFhttps://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gbk2gff converter

?[cid:part12.06090304.05060707@tamu.edu]

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.edumailto:esr@tamu.edu