On Mon, May 20, 2013 at 3:05 PM, Peter Cock <p.j.a.c...@googlemail.com>
wrote:
> On Mon, May 20, 2013 at 2:47 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> Peter wrote:
>>> Right now the single biggest class of test failures amongst my tools on
>>> the Test Tool Shed is a missing dependencies on the blast_datatypes
>>> repository: http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
>>>
>>> As a short term measure, could the dev team upload blast_datatypes
>>> to the Test Tool Shed as well please (and give me write access)? Then
>>> thanks to the recent change in [1] I can reference the dependency
>>> without explicitly naming the Tool Shed.
>>
>> I've copied the blast_datatypes from the main tool shed to the test
>> tool shed with all history in tact.  See
>>
>> http://testtoolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
>>
>>
>>>
>>> If you can do it in a way that preserves the same revision history can
>>> change set hashes even better - then I can replace this:
>>>
>>> <repository toolshed="http://toolshed.g2.bx.psu.edu";
>>> name="blast_datatypes" owner="devteam"
>>> changeset_revision="f9a7783ed7b6" />
>>>
>>> with:
>>>
>>> <repository name="blast_datatypes" owner="devteam"
>>> changeset_revision="f9a7783ed7b6" />
>>>
>>> and can use the same repository_dependencies.xml file on both Tool
>>> Sheds.
>
> Great, I'm trying that now here:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/9ef0d4ecb9d5
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/bf634ebee84c
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/2d4757de6180

Hi Greg (& Dave),

Thanks for Dave for fixing the missing test results issue,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014791.html

I can now see the effect the dependency change had -
unfortunately the blast_datatypes install seems to be
unsuccessful, but I am not seeing a helpful error from
the Tool Shed tests.

Let's focus on the simplest case, where blast_datatypes
is the only dependency:

<?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>

http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/bf634ebee84c

Automated tool test results

Tool test 
results<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&id=90191ce08fa7fc29&message=&changeset_revision=bf634ebee84c>
Automated test 
environment<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&id=90191ce08fa7fc29&message=&changeset_revision=bf634ebee84c>
*Time tested:* ~ 6 hours ago*System:* Linux 3.5.0-21-generic*Architecture:*
 x86_64*Python version:* 2.7.3*Galaxy revision:* 9821:feaab01c738a*Galaxy
database version:* 115*Tool shed revision:* 9820:f5fe2f094060*Tool shed
database version:* 19*Tool shed mercurial version:* 2.2.3
Installation errors* - no functional tests were run for any tools in this
changeset 
revision*<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&id=90191ce08fa7fc29&message=&changeset_revision=bf634ebee84c>
Repository 
dependencies<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?status=done&id=90191ce08fa7fc29&message=&changeset_revision=bf634ebee84c>
Tool shedNameOwnerChangeset revisiontesttoolshed.g2.bx.psu.edu
blastxml_to_top_descrpeterjcbf634ebee84cErrorNone




It seems that an error occurred with the dependencies, but
unfortunately all we get as the error message is "None".

Regards,

Peter
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