Problems installing PhyloPhlAn

[tayaforde]

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!

[mattbull]

You’ll definitely need scipy to be able to run PhyloPhlAn.

Please could you try installing scipy with Python2’s pip package manager:

sudo pip2 install scipy

and then trying thePhyloPhlAn command again?

[tayaforde]

Thanks for the suggestion. I have done so, and am now getting a different error message:
Traceback (most recent call last):
File “./phylophlan.py”, line 27, in
import taxcuration as taxc
File “/home/ubuntu/programs/phylophlan/taxcuration/taxcuration.py”, line 11, in
import pyphlan as circ
File “/home/ubuntu/programs/phylophlan/taxcuration/pyphlan.py”, line 1, in
from Bio import Phylo
ImportError: No module named Bio
I wonder if it might be related to the PhyloPhlAn program being in the PATH, similar to previous reported issues?
https://bitbucket.org/nsegata/phylophlan/issues/6/importerror-no-module-named-taxcuration

[mattbull]

No, its just another dependency issue I’m afraid.

sudo pip2 install biopython

should get you over that one…

[tayaforde]

In business now - thank you very much for your help!