Re: [galaxy-dev] Galaxy Tool Shed:- Uploading tool packages fails with Server Error message

2011-04-19 Thread Vipin TS 
Hi Greg,

Regarding the tools contained in fml_gff_converter_programs.tar.bz2, the
> following xml files are not well formed due to the malformed " EDIT HERE >" tag:
>
> fml_gff_converter_programs/galaxy/bed_to_gff3.xml
> fml_gff_converter_programs/galaxy/gff3_to_bed.xml
> fml_gff_converter_programs/galaxy/gff3_to_gtf.xml
> fml_gff_converter_programs/galaxy/gtf_to_gff3.xml
>
> In addition, none of these files include the required "version" attribute
> in the  tag.
>

Many thanks for pointing me the version number issue with tool configuration
file. I forgot the same.


> The same goes for the files in ~/gff_groomer/fml_gff_groomer/galaxy - they
> are not well-formed due to the same  tag, and they do
> not include the "version" attribute int the  tag.  Tools tags should
> look something like this:
>
> 
>
> I've made some enhancements to the tool shed code that will display errors
> like this ( rather than resulting in the current server error ), so the next
> time I update the tool shed ( within the next couple of days ), this problem
> will be corrected.
>
> In the meantime, if you make the above corrections, you should have no
> problems uploading your tools to the tool shed.
>
> Thanks very much for pointing out these issues, and for taking the time to
> contribute your tools to the Galaxy community.
>
>
Yes I did the changes accordingly and now it uploaded into the Tool shed.
Thanks for your quick fix.

regards, Vipin
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Re: [galaxy-dev] Galaxy Tool Shed:- Uploading tool packages fails with Server Error message

2011-04-18 Thread Greg Von Kuster 
Hello Vipin,

Regarding the tools contained in fml_gff_converter_programs.tar.bz2, the 
following xml files are not well formed due to the malformed "" tag:

fml_gff_converter_programs/galaxy/bed_to_gff3.xml
fml_gff_converter_programs/galaxy/gff3_to_bed.xml
fml_gff_converter_programs/galaxy/gff3_to_gtf.xml
fml_gff_converter_programs/galaxy/gtf_to_gff3.xml

In addition, none of these files include the required "version" attribute in 
the  tag.

The same goes for the files in ~/gff_groomer/fml_gff_groomer/galaxy - they are 
not well-formed due to the same  tag, and they do not 
include the "version" attribute int the  tag.  Tools tags should look 
something like this:



I've made some enhancements to the tool shed code that will display errors like 
this ( rather than resulting in the current server error ), so the next time I 
update the tool shed ( within the next couple of days ), this problem will be 
corrected.

In the meantime, if you make the above corrections, you should have no problems 
uploading your tools to the tool shed.

Thanks very much for pointing out these issues, and for taking the time to 
contribute your tools to the Galaxy community.

Greg Von Kuster


On Apr 18, 2011, at 3:58 PM, Vipin TS wrote:
On Apr 18, 2011, at 11:28 AM, Vipin TS wrote:

> Dear Galaxy team, 
> 
> I would like to upload a set of converter programs available for Generic 
> Feature Format (GFF). 
> When I tried to upload to Galaxy tool shed using my user name 
> vipin...@tuebingen.mpg.de, it gives me Server error message. 
> I am using a *.bz2 file for uploading. It will be great if you can have a 
> look on this issue.
> 
> thanks in advance, 
> Vipin T S
> Friedrich Miescher Laboratory 
> of the Max Planck Society
> Spemannstrasse 39, 72076 
> Tuebingen, Germany
> Tel:+49 7071 601 824
> 
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



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Re: [galaxy-dev] Galaxy Tool Shed:- Uploading tool packages fails with Server Error message

2011-04-18 Thread Jennifer Jackson 

Hello Vipin,

To confirm, you are following the instructions at:
http://community.g2.bx.psu.edu/ -> Help -> How to upload [..]

And using "Upload a tool"?

If the size is large (close to 2G or larger), are you using an http or 
ftp load? A browser file load will likely fail due to a time-out. Is 
this the server error you encountered? Is so, please try the other method.


Hopefully this helps to resolve the issue, but if the problem is with 
HTTP/FTP please provide us with more details so that we can 
troubleshoot. You can send private information (the URL) and what steps 
you are following directly to me.


Best,

Jen
Galaxy team

On 4/18/11 8:28 AM, Vipin TS wrote:

Dear Galaxy team,

I would like to upload a set of converter programs available for Generic
Feature Format (GFF).
When I tried to upload to Galaxy tool shed using my user name
vipin...@tuebingen.mpg.de , it gives
me Server error message.
I am using a *.bz2 file for uploading. It will be great if you can have
a look on this issue.

thanks in advance,
Vipin T S
Friedrich Miescher Laboratory
of the Max Planck Society
Spemannstrasse 39, 72076
Tuebingen, Germany
Tel:+49 7071 601 824



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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
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