cannot install prodigal (mac os catalina 10.15.7)

[mikeds211]

pip install worked fine except for the notification that prodigal could not be installed. The notification window offered the option to install it but that only gave another error window with "Error while downloading Prodigal: argument should be string, bytes or integer, not PosixPath". So I installed prodigal myself, checked it worked from the terminal and then reopened phagecom. It still cannot see prodigal. Do I need to set a specific path for phagecom to see prodigal (which is sitting in /usr/local/bin) or is the version of Prodigal too old? It is V2.6.3: February, 2016. UPDATE: I was using python 3.5 so I updated to 3.9. Reinstalled phage-commander. Now I have more serious problems. First the installation log, which proceeded successfully:

~ % pip install phage-commander Collecting phage-commander Using cached phage_commander-0.4.5.dev0-py3-none-any.whl (65 kB) Requirement already satisfied: ruamel.yaml in ./opt/miniconda3/lib/python3.8/site-packages (from phage-commander) (0.16.12) Requirement already satisfied: requests in ./opt/miniconda3/lib/python3.8/site-packages (from phage-commander) (2.25.0) Requirement already satisfied: openpyxl in ./opt/miniconda3/lib/python3.8/site-packages (from phage-commander) (3.0.5) Requirement already satisfied: bs4 in ./opt/miniconda3/lib/python3.8/site-packages (from phage-commander) (0.0.1) Requirement already satisfied: pyqt5 in ./opt/miniconda3/lib/python3.8/site-packages (from phage-commander) (5.15.2) Requirement already satisfied: biopython in ./opt/miniconda3/lib/python3.8/site-packages (from phage-commander) (1.78) Requirement already satisfied: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.9" in ./opt/miniconda3/lib/python3.8/site-packages (from ruamel.yaml->phage-commander) (0.2.2) Requirement already satisfied: chardet<4,>=3.0.2 in ./opt/miniconda3/lib/python3.8/site-packages (from requests->phage-commander) (3.0.4) Requirement already satisfied: idna<3,>=2.5 in ./opt/miniconda3/lib/python3.8/site-packages (from requests->phage-commander) (2.10) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./opt/miniconda3/lib/python3.8/site-packages (from requests->phage-commander) (1.25.11) Requirement already satisfied: certifi>=2017.4.17 in ./opt/miniconda3/lib/python3.8/site-packages (from requests->phage-commander) (2020.11.8) Requirement already satisfied: jdcal in ./opt/miniconda3/lib/python3.8/site-packages (from openpyxl->phage-commander) (1.4.1) Requirement already satisfied: et-xmlfile in ./opt/miniconda3/lib/python3.8/site-packages (from openpyxl->phage-commander) (1.0.1) Requirement already satisfied: beautifulsoup4 in ./opt/miniconda3/lib/python3.8/site-packages (from bs4->phage-commander) (4.9.3) Requirement already satisfied: PyQt5-sip<13,>=12.8 in ./opt/miniconda3/lib/python3.8/site-packages (from pyqt5->phage-commander) (12.8.1) Requirement already satisfied: numpy in ./opt/miniconda3/lib/python3.8/site-packages (from biopython->phage-commander) (1.19.4) Requirement already satisfied: soupsieve>1.2; python_version >= "3.0" in ./opt/miniconda3/lib/python3.8/site-packages (from beautifulsoup4->bs4->phage-commander) (2.0.1) Installing collected packages: phage-commander Successfully installed phage-commander-0.4.5.dev0

[and here the startup log] ~ % phagecom Traceback (most recent call last): File "/Users/mdyallsm/opt/miniconda3/bin/phagecom", line 5, in from phagecommander.phagecom import main File "/Users/mdyallsm/opt/miniconda3/lib/python3.8/site-packages/phagecommander/init.py", line 1, in from phagecommander import Gene, phagecom File "/Users/mdyallsm/opt/miniconda3/lib/python3.8/site-packages/phagecommander/Gene.py", line 19, in from Bio.Alphabet import IUPAC File "/Users/mdyallsm/opt/miniconda3/lib/python3.8/site-packages/Bio/Alphabet/init.py", line 20, in raise ImportError( ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information."

[ptsourkas]

Hi, the updated version of Phage Commander has resolved this issue and is available at https://github.com/sarah-harris/PhageCommander.