It turns out there were two problems. First, the test environment was not resolving the upload tool's dependency on samtools, which I've now corrected. Second, the bam file detection on upload was broken due to the bug in python 2.7.4's gzip module, which I've also corrected.
I have re-run the test framework on samtools_idxstats, and it has now passed its test.
On 11/14/2013 11:27 AM, Peter Cock wrote:
On Wed, Nov 13, 2013 at 12:03 PM, Greg Von Kuster firstname.lastname@example.org wrote:
Yesterday we discovered what Björn has communicated and added it to the Trello card for this issue:
becomes the following in your renamed tool_dependencies.xml file:
<tool_dependency> <package name="samtools" version="0.1.9"> <repository name="package_samtools_0_1_19" owner="iic" /> </package> </tool_dependency>
This is all discussed in the following section of the Tool Shed wiki:
I believe that is what I did in response to Bjoern's email, shortly before seeing your email (but thank you for the detailed reply):
As an aside, I personally I find the tool_dependencies.xml vs repository_dependecies.xml split confusing when defining a dependency on a third party tool which is provided by another Tool Shed repository. I don't understand why this isn't all done with repository_dependecies.xml alone.
Let me know if this doesn't correct this problem.
Last night's Test Tool Shed run confirms this does NOT fix the problem, which does indeed appear to be in the Galaxy upload tool which has an implicit dependency on samtools for indexing BAM files as John suggested.
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