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mothur datatypes: don't generate error for pairwise distance matrices #2489

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merged 1 commit into from Jun 13, 2016

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commented Jun 10, 2016

pairwise distance matrices don't (always) have the number of sequences on the first line, so don't generate an error

ping @bgruening (without this some of the mothur tests will still fail)

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commented Jun 10, 2016

@shiltemann this is only a warning. Why does the tool fail with a warning?
Still - looks good to me.

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commented Jun 10, 2016

not sure, but planemo fails on this and if I upload in interface it also turns red ..don't know if anything changed recently, because I could have sworn this didn't fail earlier

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commented Jun 10, 2016

I will leave this open for @jmchilton or @martenson. Maybe this is a regression.

@galaxybot galaxybot added the triage label Jun 10, 2016

@galaxybot galaxybot added this to the 16.07 milestone Jun 10, 2016

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commented Jun 13, 2016

Logging to standard error during metadata generation is problematic - many Galaxy jobs including upload1 jobs are configured to fail on stuff being written to standard error. I thought there was an open issue to allow logging during metadata generation but I can't find it.

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@bgruening bgruening merged commit c797d2b into galaxyproject:dev Jun 13, 2016

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commented Jun 13, 2016

Thanks @jmchilton for clarification.

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