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