'bp_genbank2gff3' installation error and running error

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'bp_genbank2gff3' installation error and running error

Wang, Xiaofei

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? 






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? 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.


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




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Re: 'bp_genbank2gff3' installation error and running error

Eric Rasche-2
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.




___________________________________________________________
Please keep all replies on the list by using "reply all"
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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
[hidden email]

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Re: 'bp_genbank2gff3' installation error and running error

Wang, Xiaofei

​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 <[hidden email]>
Sent: Thursday, January 28, 2016 4:40 PM
To: Wang, Xiaofei; [hidden email]
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.




___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Ciao,
Eric
-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
[hidden email]

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/