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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
GNU General Public License v2.0
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minimap2 dependency #231

Closed delfair closed 5 years ago

delfair commented 5 years ago

Hello Torsten, Excellent software. I'm enjoying (and learning a lot) using nullarbor and your other programs. I had a small issue with a dependency on minimap2 (https://github.com/lh3/minimap2). Without this the pipeline runs (with make -k option) but the report directory isn't created at the end. Easily fixed after examining the log file, but nullarbor.pl --check doesn't check for minimap2 so this might save someone some time... Del

tseemann commented 5 years ago

Nullarbor does not depend on minimap2 itself, but one of it's dependencies does: Snippy 4.x. It is assumed you have all the dependences working when you run nullarbor.pl --check.

What does snippy --check say?

I strongly recommend the use of bioconda or brew to install this complicated piece of software.