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antoniojbt / project_quickstart

Boilerplate tools and templates for setting up a data analysis project.
GNU General Public License v3.0
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python xxxx/pipeline_pq_example.py plot full requires dot #11

Open antoniojbt opened 5 years ago

antoniojbt commented 5 years ago

For the cgat-core based pipeline, the command: python ../code/pq_example/pipeline_pq_example/pipeline_pq_example.py plot full

gives:

Traceback (most recent call last):
  File "../code/pq_example/pipeline_pq_example/pipeline_pq_example.py", line 473, in <module>
    sys.exit(P.main(sys.argv))
  File "/opt/conda/envs/pq_test/lib/python3.7/site-packages/cgatcore/pipeline/control.py", line 1390, in main
    run_workflow(options, args)
  File "/opt/conda/envs/pq_test/lib/python3.7/site-packages/cgatcore/pipeline/control.py", line 1286, in run_workflow
    checksum_level=options.ruffus_checksums_level)
  File "/opt/conda/envs/pq_test/lib/python3.7/site-packages/ruffus/task.py", line 4137, in pipeline_printout_graph
    signal_callback=is_node_up_to_date)
  File "/opt/conda/envs/pq_test/lib/python3.7/site-packages/ruffus/graph.py", line 1155, in graph_printout
    retcode, cmd + "\n" + "\n".join([str(result_str), str(error_str)]))
subprocess.CalledProcessError: Command 'dot -Gsize='(11,8)'  -Tsvg < /tmp/tmpy87tn_3t.dot
b''
b'/bin/sh: 1: dot: not found\n'' returned non-zero exit status 127.
(pq_test) root@4782c8cbdd5e:/pq_example/results# dot
bash: dot: command not found