Hello Birgit, Your archive included several "._" scripts for some reason. None of these were valid xml files, but since they have a .xml extension, the tool shed attempts to parse them which results in the error message you got: not well-formed (invalid token): line 1, column 0 Here is the contents of your achive: -rw-r--r-- 1 gvk wheel 6148 Jun 6 16:09 .DS_Store -rw-r--r-- 1 gvk wheel 171 May 25 13:44 ._Calculate_TestVariants_Variant_Frequencies.xml -rwxr-xr-x 1 gvk wheel 171 May 3 19:19 ._Calculate_TestVariants_Variant_Frequencies_0_1_0.pl -rw-r--r-- 1 gvk wheel 171 May 31 13:39 ._List_Unique_Variants.xml -rwxr-xr-x 1 gvk wheel 171 May 3 12:50 ._List_Unique_Variants_2_1_0.pl -rw-r--r-- 1 gvk wheel 1950 May 25 13:44 Calculate_TestVariants_Variant_Frequencies.xml -rwxr-xr-x 1 gvk wheel 9242 May 3 19:19 Calculate_TestVariants_Variant_Frequencies_0_1_0.pl -rw-r--r-- 1 gvk wheel 13625 May 31 13:39 List_Unique_Variants.xml -rwxr-xr-x 1 gvk wheel 22321 May 3 12:50 List_Unique_Variants_2_1_0.pl I eliminated all of the "._" files and created a new archive which uploaded successfully. I've attached the archive. Greg Von Kuster On Jun 12, 2012, at 4:38 PM, Birgit Crain wrote:
Thanks, Greg
I tried uploading the same tar ball without the tool_data_table_config.xml.sample file and the tools load fine (to troubleshoot I added only tools that actually do not depend on the file). As soon as I add the .sample file to the tar ball I get the error message.
Thanks, Birgit
From: Greg Von Kuster <greg@bx.psu.edu> Date: Tuesday, June 12, 2012 1:18 PM To: Birgit Crain <bcrain@completegenomics.com> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample
Hi Birgit,
I don't see any problem with your xml definition below. Are you sure the problem is not with another file in the tarball? If you can send me the tarball, I'll take a look.
Greg Von Kuster
On Jun 12, 2012, at 4:09 PM, Birgit Crain wrote:
Hi
I'm developing tools that use an entry in the tool_data_table_config.xml file. For upload into a repository I created a tool_data_table_config.xml.sample file with the corresponding table entry. The structure for the file I copied from the tool_data_table_config.xml. in the galaxy download.
<tables> <!-- Start location of cgatools crr files --> <table name="cg_crr_files" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/cg_crr_files.loc" /> </table> <!-- End Location of cgatools crr files --> </tables>
When I upload the tar ball into the repository the tools won't load properly and I get the following message:
not well-formed (invalid token): line 1, column 0
Any suggestions what I'm missing or how to fix this error?
Thanks, Birgit
The contents of this e-mail and any attachments are confidential and only for use by the intended recipient. Any unauthorized use, distribution or copying of this message is strictly prohibited. If you are not the intended recipient please inform the sender immediately by reply e-mail and delete this message from your system. Thank you for your co-operation. ___________________________________________________________ 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:
The contents of this e-mail and any attachments are confidential and only for use by the intended recipient. Any unauthorized use, distribution or copying of this message is strictly prohibited. If you are not the intended recipient please inform the sender immediately by reply e-mail and delete this message from your system. Thank you for your co-operation. <scripts.tar.gz>___________________________________________________________ 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: