SourceTracker2

Question

[Giulia.cosenza]

Hi everyone, It's my first time using sourcetracker2.

I've installed the software with Conda with the following commands:

> conda create -n st2 -c biocore python=3.5 numpy scipy scikit-bio biom-format h5py hdf5 seaborn

> conda activate st2

> pip install sourcetracker

But when I try to use it, even with the simplest command:

sourcetracker2 gibbs --help

I obtain this huge error:

"Traceback (most recent call last):
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/bin/sourcetracker2", line 6, in 
from sourcetracker._cli import cli
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/sourcetracker/_cli/init.py", line 19, in 
import_module('sourcetracker._cli.gibbs')
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/sourcetracker/_cli/gibbs.py", line 23, in 
from sourcetracker._sourcetracker import (
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/sourcetracker/_sourcetracker.py", line 15, in 
from skbio.stats import subsample_counts
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/skbio/init.py", line 13, in 
import skbio.io # noqa
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/skbio/io/init.py", line 238, in 
import_module('skbio.io.format.lsmat')
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/skbio/io/format/lsmat.py", line 77, in 
from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/skbio/stats/distance/init.py", line 192, in
from ._base import (DissimilarityMatrixError, DistanceMatrixError,
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 13, in 
from IPython.core.pylabtools import print_figure
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/IPython/init.py", line 55, in 
from .terminal.embed import embed
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/IPython/terminal/embed.py", line 16, in 
from IPython.terminal.interactiveshell import TerminalInteractiveShell
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/IPython/terminal/interactiveshell.py", line 18, in 
from prompt_toolkit.enums import DEFAULT_BUFFER, EditingMode
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/prompt_toolkit/init.py", line 16, in 
from .application import Application
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/prompt_toolkit/application/init.py", line 1, in 
from .application import Application
File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/prompt_toolkit/application/application.py", line 255

self.full_screen: bool = full_screen

             ^

SyntaxError: invalid syntax

What should I do ?

Is there another way to use this software?

Thank you !

[Zina]

Hi! I got the same error message. Scrolling the installation messages I have realized that I needed it to install cython first. You can run this piece of code: pip install Cython --install-option="--no-cython-compile"
and then retry. It should work. Cheers