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tanghaibao / jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics
BSD 2-Clause "Simplified" License
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ALLMAPS errors running test data #356

Closed jguppy closed 3 years ago

jguppy commented 3 years ago

Hi, I've recently been trying to install and run ALLMAPs but have been running into a few errors. I've followed the installation guide on the wiki on both a local linux machine and a uni HPC server and have come across the following syntax error when trying to use the shell script calling allmaps.py.

image

I've taken a look through the allmaps.py script itself (v1.1.7) and proceeding the code I couldn't see any obvious issues, however when looking back at the earlier version (v1.1.5) i noticed that line 7 "from future import print_function" was removed. Replacing this line in the allmaps.py script allowed me to pass the syntax error. Does this make sense for me to do in context with the syntax error?

After this a second error has now come up -> Traceback (most recent call last): File "allmaps2.py", line 21, in from more_itertools import flatten, pairwise ImportError: No module named more_itertools

Is this a new dependency not covered in the wiki page that I should install?

Thanks for your help here,

Jarrod Guppy

tanghaibao commented 3 years ago

@jguppy

Sorry for the inconvenience. We are dropping Python 2 support. Please move to Python 3 if possible.

Haibao

jguppy commented 3 years ago

Thanks @tanghaibao I should have thought to check that myself. Looks to have solved it. As a FYI for others users I needed to install the following modules with pip3 in addition to those listed the wiki page instructions. more-itertools dataclasses natsort rich brewer2mpl

Thanks again for your help

tanghaibao commented 3 years ago

@jguppy

Thanks for the notes. I was hoping when you do:

pip3 install -U jcvi

All these dependencies should be installed automatically for you.

Haibao