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there are fewer than 4 unique species, then the filter is not used, and all genomes will be used for initial steps
failing when there are duplicate genome names with different ids. Also adding list of ids to the JSON output
changes for PATRIC version
Fixes missing labels on pepr run for PATRIC
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This PR includes changes required for the PATRIC installation:
Don't use hardcoded binary path; instead use the PATH environment.
Add return-code logging of invoked programs, and emit the stderr output if the return code is not zero.
Change the muscle invoked to the command muscle-3.6 since that is the precise version required.
In the bootstrap build we only use the minimal set of binaries from the repo since several do not run on 64-bit Centos. However, correct execution appears to be sensitive to some of the tool versions (my current guess the raxml version is important.)