This checks that the external dependencies are found and that their versions are high enough.
The usage is:
(there are no options).
Ideally, the output will look something like this:
Using bwa version 0.7.12 as /bin/bwa
Using nucmer version 3.1 as /bin/nucmer
Using prodigal version 2.60 as /bin/prodigal
Using samtools version 0.1.19 as /bin/samtools
Using spades version 3.5.0 as /bin/spades.py
Otherwise, there will be error messages. For example:
Version of bwa too low. I found 0.6.2, but must be at least 0.7.12. Found here:
/bin/bwa
Using nucmer version 3.1 as /bin/nucmer
Using prodigal version 2.60 as /bin/prodigal
Using samtools version 0.1.19 as /bin/samtools
Didn't find spades in path. Looked for:spades.py
In this case, Circlator was unable to find SPAdes in the user's path. It found BWA, but the version was too low. The remaining tools were OK.
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