I am trying to install PhyloPhlAn (https://huttenhower.sph.harvard.edu/phylophlan) on a GVL VM “bacterial-genomics” hosted at Swansea. I downloaded the program using the following command:
hg clone https://bitbucket.org/nsegata/phylophlan
and downloaded the required dependencies (usearch, muscle and FastTree), which I have put in /usr/local/bin/
When I try to run the program using the test data provided (see Example 1 on the PhyloPhlAn website), I get the following error message:
Traceback (most recent call last): File "./phylophlan.py", line 27, in <module> import taxcuration as taxc File "taxcuration/taxcuration.py", line 8, in <module> from scipy import stats ImportError: No module named scipy
Scipy isn’t listed among the program dependencies, and it seems to be already installed on the VM (v1.0.1). Any suggestions for troubleshooting would be much appreciated!