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 [Screen Shot 2015-12-30 at 3.58.03 PM.png] to my local galaxy. But I got an error as below.
Does it associated with dependencies? I see it needs these [Screen Shot 2015-12-30 at 4.00.33 PM.png] . 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.
[Screen Shot 2015-12-30 at 3.50.14 PM.png]
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 https://galaxy.cbio.mskcc.org/tool_runner?tool_id=gff_examine file Parent-Child relations FeatureScan https://galaxy.cbio.mskcc.org/tool_runner?tool_id=gff_available_limits gives an overview about GFF feature content CONVERTER PROGRAMS GTF_to_GFF3 https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gtf2gff3 converter BED_to_GFF3 https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_bed2gff converter GFF3_to_BED https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gff2bed converter GBK-to-GFF https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gbk2gff converter
[Screen%20Shot%202015-12-30%20at%204.09.57%20PM.png]
Thanks!
Best,
Xiaofei
Apologies for the lack of help Xiaofei. Good luck getting it all to work.
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Ciao, Eric
