Hello Peter,

On May 23, 2013, at 4:49 AM, Peter Cock wrote:

> On Wed, May 22, 2013 at 9:59 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> 
>> I cannot guarantee it, but this may be related to a fix I just committed
>> that populates the <repository> tag in the dependency definitions with a
>> toolshed attribute if it is missing (it looks like it is in your case).  I
>> used to not populate the tag, but simply stored the tool shed in the
>> repository metadata.  Bjorn discovered, however, that certain repository
>> installations would not succeed if the toolshed attribute was missing.  WHen
>> I investigated this, I discovered  that some downstream stuff could not
>> locate the appropriate tool shed if the attribute was missing from the tag.
>> 
>> I fixed this in 9836:252027d00b44 by populating this tag attribute if it
>> was missing.  Unfortunately, a new dependency definition has to be uploaded
>> to those repositories that have definitions where it is not set in order to
>> get this fix.
>> 
>> I don't know if updating your dependency file in this repository will fix
>> this issue, but just wanted to alert you to this.
>> 
>> Very sorry for any inconvenience!
>> 
>> Greg Von Kuster
> 
> Finger's crossed - I've changed repository_dependencies.xml by
> updating the comment in it,
> 
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/bb81d3afa28d
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/482b7f4d3587
> 
> As an aside, the XML comment line seems not to show up properly
> in the HTML diff view on the toolshed for this change. For example:


Yes, comments were stripped out and not saved.  However, I've committed a fix 
for this issue in 9844:0acfbcd4235b, so all future comments should be saved.  
Sorry for the inconvenience of losing any comments you had previously.


> 
> Commit message:
> Uploaded v0.0.20 preview 8, update comment in dependencies XML
> modified:
> tools/ncbi_blast_plus/repository_dependencies.xml
> tools/ncbi_blast_plus/repository_dependencies.xml
> --- a/tools/ncbi_blast_plus/repository_dependencies.xmlMon May 20
> 10:04:51 2013 -0400
> +++ b/tools/ncbi_blast_plus/repository_dependencies.xmlThu May 23
> 04:47:28 2013 -0400
> @@ -1,5 +1,5 @@
> <?xml version="1.0"?>
> <repositories description="This requires the BLAST datatype
> definitions (e.g. the BLAST XML format).">
> -<!-- Revision 4:f9a7783ed7b6 on the main tool shed is v0.0.14 which
> added BLAST databases -->
> -<repository name="blast_datatypes" owner="devteam"
> changeset_revision="f9a7783ed7b6" />
> -</repositories>
> +
> +<repository changeset_revision="f9a7783ed7b6" name="blast_datatypes"
> owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu"; />
> +</repositories>
> \ No newline at end of file
> 
> That first "plus" line should give the new comment, i.e.
> 
> <!-- Revision 4:f9a7783ed7b6 on the main (and test) tool shed is
> v0.0.14 which added BLAST databases -->
> 
> Regards,
> 
> Peter


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