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denglab / SeqSero2

SeqSero2
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Add --check option to ensure all dependencies are installed #9

Closed tseemann closed 3 years ago

tseemann commented 5 years ago

For example:

% seqsero2 --check
Using bwa - /home/linuxbrew/.linuxbrew/bin/bwa | Version: 0.7.17-r1188
Using pigz - /home/linuxbrew/.linuxbrew/bin/pigz | pigz 2.4
Using samtools - /home/linuxbrew/.linuxbrew/bin/samtools | Version: 1.9 (using htslib 1.9)
Using skesa - /home/linuxbrew/.linuxbrew/bin/skesa | SKESA v.2.3.0
Using spades.py - /home/linuxbrew/.linuxbrew/bin/spades.py | SPAdes v3.13.0

or

ERROR: can not find "samtools" in PATH