I tried a few times to install humann2 on Mac OSX.
I followed the tutorial that is on Github page.
Here are the steps that I followed and the error that ensued:
I downloaded humann2 from pip as follow:
pip install humann2 --no-binary :all:
I tried to run a demo using the following command:
humann2 --input examples/demo.fastq --output $OUTPUT_DIR
Even when doing this I am still getting the following error:
“CRITICAL ERROR: The bowtie2 executable can not be found. Please check the install.”
It looks like even when downloading from the source it still did not find the essential software.
- I installed bowtie2 manually following the steps in their website:
_ Download the source code (by paying attention that the version is compatible with humann2)
_ brew install tbb
=> The previous error got resolved but instead this time it was:
”CRITICAL ERROR: The diamond executable can not be found.”
Installing diamond have been fruitless as well with the same critical error but I was able to resolve that error by downloading an old version of diamond (v0.8.22)
But now I have a critical error saying:
“CRITICAL ERROR: metaphlan2 executable can not be found”
However when doing the following command:
metaphlan2.py —version it looks it is defined and accessible within the path.
Trying to get older versions of metaphlan2 or Humann2 did not solve the issue.
Could you provide some support? What was the version of the different dependencies at the time of the tutorial?