Question: planemo test - mysterious samtools dependency
0
gravatar for esch0041
9 months ago by
esch004160
esch004160 wrote:

When I run planemo test for a tool that has declared no dependencies on samtools, I nevertheless see the following in the output

2018-01-08 19:01:58,214 DEBUG [galaxy.tools.deps] Building dependency shell command for dependency 'samtools' 2018-01-08 19:01:58,215 DEBUG [galaxy.tools.deps] Find dependency samtools version None

Is there a way to tell planemo not to look for samtools?

planemo • 243 views
ADD COMMENTlink modified 9 months ago by jmchilton1.1k • written 9 months ago by esch004160
1
gravatar for jmchilton
9 months ago by
jmchilton1.1k
United States
jmchilton1.1k wrote:

That message I think it generated from the upload tool - it shouldn't break your tests as long as you aren't uploading bam files as inputs to the tool tests and can safely be ignored in most cases. The next version of Galaxy will no longer have a samtools dependency as part of the upload process at all so this message will go away also. Thanks for using Planemo!

ADD COMMENTlink written 9 months ago by jmchilton1.1k
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