On Mon, May 20, 2013 at 3:05 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, May 20, 2013 at 2:47 PM, Greg Von Kuster <greg@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/bf634eb...
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/bf634eb... 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