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.ts@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
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.ts@tuebingen.mpg.de mailto:vipin.ts@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
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:
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 "<! -- TODO 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 <tool> tag.
The same goes for the files in ~/gff_groomer/fml_gff_groomer/galaxy - they are not well-formed due to the same <! -- TODO EDIT HERE > tag, and they do not include the "version" attribute int the <tool> tag. Tools tags should look something like this:
<tool id="fml_bed2gff" name="BED_to_GFF3" version="1.0.0">
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.ts@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
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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 "<! -- TODO 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 <tool> 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 <! -- TODO EDIT HERE > tag, and they do not include the "version" attribute int the <tool> tag. Tools tags should look something like this:
<tool id="fml_bed2gff" name="BED_to_GFF3" version="1.0.0">
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
galaxy-dev@lists.galaxyproject.org
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Greg Von Kuster -
Jennifer Jackson -
Vipin TS