On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
On Jan 29, 2014, at 1:18 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Peter wrote:
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr 2014-01-29 missing blast_datatypes dependency (why?) 2014-01-28 showing failed tests for sambamba_filter (wrong tool)
I'll have to take a look at the above issue. I'm completely swamped though, so it will be a while.
I believe I have the above issue resolved in 12331:fd4936ae8219 ( at least I took a step in the right direction ). We'll have to wait for tonight's test run to make sure everything is handled correctly.
Hi again Greg, That one is still weird - was that fix deployed to the main toolshed? http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr Moreover there is a similar problem with the matching repository on the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr 2014-01-04 showing failed tests for proteomics_search_tandem_1 2013-12-20 showing failed tests for proteomics_search_tandem_1 2013-12-18 tests for blastxml_to_top_descr passed 2013-12-17 tests for blastxml_to_top_descr passed -- Returning to the MIRA4 problem, I got a meaningful test failure which I fixed (I hadn't set an environment variable in the install script), but I now get only partial test output: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Not datestamped (a glitch if there is only one test entry?): Automated tool test results Automated test environment Time tested: 2014-02-03 16:25:08 System: Architecture: Python version: Galaxy revision: Galaxy database version: Tool shed revision: 12332:d9f6f3f24671 Tool shed database version: 22 Tool shed mercurial version: 2.2.3 Tools missing tests or test data Tool id: mira_4_0_mapping Tool version: 0.0.2 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_mapping/0.0.2 Missing components: Functional test definitions missing for mira_4_0_mapping. Tool id: mira_4_0_de_novo Tool version: 0.0.2 Tool guid: testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_de_novo/0.0.2 Missing components: Functional test definitions missing for mira_4_0_de_novo. That's all fine, but where are the test results for mira_bait which I would expect to pass? Thanks, Peter