dmnfarrell / pybioviz Goto Github PK

Hello,
This package looks amazing! I am trying to install it and just wanted to bring to your attention the error I am getting when trying to install the extensions:

An error occured.
ValueError: Please install nodejs 5+ and npm before continuing installation. nodejs may be installed using conda or directly from the nodejs website.
See the log file for details: /var/folders/d7/8vn6rd1d6f37gtgy_13h3b95mx3fmv/T/jupyterlab-debug-gpa6bos_.log
An error occured.
ValueError: Please install nodejs 5+ and npm before continuing installation. nodejs may be installed using conda or directly from the nodejs website.
See the log file for details: /var/folders/d7/8vn6rd1d6f37gtgy_13h3b95mx3fmv/T/jupyterlab-debug-403256tw.log

The command below installed NodeJs from within the Jupyter notebook:

conda install nodejs

Cheers!

Has this package been updated to recent Bokeh versions? What are the versions compatibles? I'm getting several errors especially with plot_sequence_alignment that could be linked to this...

Hi,
I am having trouble installing this package in a Google Colab Notebook. I first tried installing it using 'pip install pybioviz', but it comes back with an error message (ERROR: No matching distribution found for pybioviz). It appears to work when I try installing it following the installation line recommended on the github page ('pip install -e git+https://github.com/dmnfarrell/pybioviz.git#egg=pybioviz'). However, if I try importing the package following the documentation page's usage section, it comes back with an error (ModuleNotFoundError: No module named 'pybioviz'). Do you have any suggestions to fix this issue?
Thanks!

I'm getting "Muscle not installed?" printed to stdout when trying to run pybioviz align -f myfile.fas on a *.fas file.

Also this same message is printed to stdout when running inside a jupyter notebook with the example you provide:

import panel as pn
#need to load panel extension first
pn.extension()
from pybioviz import dashboards
app = dashboards.sequence_alignment_viewer('file.fa') 

I have no idea what "muscle" is

I have only been able to find documentation for producing one of your example plots ("sequence allignment viewer").

I would like to know how to make other plots. For example, to view allignment from bam files which you show figure for.

Please could provide some more code examples?