ModuleNotFoundError: No module named 'graphviz'

[memathyer]

After successfully running the ATAC-seq pipeline through the Conda environment, Croo was unable to organize my output as it was unable to find the module 'graphviz'. I assumed this was something automatically installed during the installation of Croo through the installation and activation of the pipeline's Conda environment, but if not, is this something I am supposed to manually install? Thanks!

(encode-atac-seq-pipeline) [mary.mathyer@login01 atac-seq-pipeline]$ croo atac/ba3ff901-3b83-4498-9f30-951aec6c0c86/metadata.json --out-def-json IVL_n4_output.json --out-dir IVL_n4_output --method {copy} Traceback (most recent call last): File "/home/mary.mathyer/miniconda3/envs/encode-atac-seq-pipeline/bin/croo", line 11, in from croo.croo import main File "/home/mary.mathyer/miniconda3/envs/encode-atac-seq-pipeline/lib/python3.7/site-packages/croo/croo.py", line 17, in from .croo_html_report import CrooHtmlReport File "/home/mary.mathyer/miniconda3/envs/encode-atac-seq-pipeline/lib/python3.7/site-packages/croo/croo_html_report.py", line 11, in from .croo_html_report_task_graph import CrooHtmlReportTaskGraph File "/home/mary.mathyer/miniconda3/envs/encode-atac-seq-pipeline/lib/python3.7/site-packages/croo/croo_html_report_task_graph.py", line 11, in from graphviz import (Source, render) ModuleNotFoundError: No module named 'graphviz'

[leepc12]

Just released v0.3.2. Please reinstall Croo.

pip unistall croo
pip install croo

This will install graphviz. But PIP-installing graphviz doesn't seem to install graphviz's executable dot.

Check Croo's version.

croo -v

You can also completely disable this task graph feature

croo ... --no-graph

[memathyer]

Reinstalling Croo worked. Thanks!