No module named 'graphviz'

[nicolerg]

Hello, I using Croo v0.3.1 installed in the conda environment with encode-atac-seq-pipeline v1.5.4. It looks like graphviz needs to be added as a dependency:

Traceback (most recent call last):
  File "/labs/smontgom/nicolerg/miniconda3/envs/encode-atac-seq-pipeline/bin/croo", line 11, in <module>
    from croo.croo import main
  File "/labs/smontgom/nicolerg/miniconda3/envs/encode-atac-seq-pipeline/lib/python3.7/site-packages/croo/croo.py", line 17, in <module>
    from .croo_html_report import CrooHtmlReport
  File "/labs/smontgom/nicolerg/miniconda3/envs/encode-atac-seq-pipeline/lib/python3.7/site-packages/croo/croo_html_report.py", line 11, in <module>
    from .croo_html_report_task_graph import CrooHtmlReportTaskGraph
  File "/labs/smontgom/nicolerg/miniconda3/envs/encode-atac-seq-pipeline/lib/python3.7/site-packages/croo/croo_html_report_task_graph.py", line 11, in <module>
    from graphviz import (Source, render)
ModuleNotFoundError: No module named 'graphviz'

pip install graphviz within the conda environment fixed it.

[leepc12]

This is already fixed in 0.3.2.

[annashcherbina]

As of 0.3.3 you also have to run apt-get install graphviz (or equivalent for your operating system), as pygraphviz does not place the dot program on the PATH by default. If using anaconda, you can also run conda install pydot-ng in addition to conda install pygraphviz.

@leepc12 you might consider adding pydot-ng as a dependency or clarifying in the docs that pygraphviz by itself will not give you the needed dot utility and the user must also install dot.

@nicolerg if you're usinig sherlock, you can run module load viz graphviz

[leepc12]

conda install pydot-ng -c anaconda conflicts with packages in requirements.txt for two ENCODE pipelines (atac/chip). Also anaconda is not an official Conda repo since 4.7.

Try apt install graphviz if you can sudo or add --no-graph to the command line.