Peter,

Thanks for bringing this to our attention, we're working on fixing a number of issues with the test framework, and hope to have more information for you tomorrow.

--Dave B.

On 2013-11-11 06:11, Peter Cock wrote:

Hi Dave,

I think this is a new regression from the Test Tool Shed installation framework,

http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/f2478dc77ccb

Tool test results Automated test environment Tools missing tests or test data Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion blast+ package 2.2.27 Error ("Invalid file %s specified, ignoring set_environment_for_install action.",/ToolDepsTest/blast+/2.2.27/iuc/package_blast_plus_2_2_27/eab09bc4d63e/env.sh)

Is that really a comma in the path? Is this a simple typo in a config file?

Note this tool is using: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_27/eab09bc... (using platform specific actions)

--

Meanwhile, over on the main Tool Shed, which I would like to update to use arch-specific actions for the packages (since that is now in the stable Galaxy releases), and switch from BLAST+ 2.2.26 to 2.2.27, we have a different install failure:

http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/70e7dcbf6573 still using 2.2.26 via shell magic, http://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26/40c69b76b46... /bin/sh: 1: blastn: not found

Peter

On Thu, Nov 14, 2013 at 4:35 PM, Peter Cock p.j.a.cock@googlemail.com wrote:

Hi Dave,

Good news, the BLAST+ tests appear to have all passed on the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/f2478dc77ccb

...

Over on the main Tool Shed, the binary installation seems to be failing (still using the bash script magic - is the test system still missing bash, or is there a different problem here?). Here too, there doesn't seem to be any mention of the tools missing tests.

At this point (given it is working on the Test Tool Shed), I think it should be safe to update the BLAST+ packages to use the new architecture/os specific <action> tags (a recent feature which is now supported in the stable Galaxy releases):

http://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26 http://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_27 http://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_28

I've just done that on the main Tool Shed, fingers crossed that will give a green light on the overnight test results for the BLAST+ wrappers.

Peter