umccr / cwl-novice-tutorial Goto Github PK

 $ mamba install cwltool graphviz wget git nodejs
Traceback (most recent call last):
  File "/Users/kanwals/miniconda/envs/cwltutorial/bin/mamba", line 7, in <module>
    from mamba.mamba import main
  File "/Users/kanwals/miniconda/envs/cwltutorial/lib/python3.11/site-packages/mamba/mamba.py", line 49, in <module>
    import libmambapy as api
  File "/Users/kanwals/miniconda/envs/cwltutorial/lib/python3.11/site-packages/libmambapy/__init__.py", line 7, in <module>
    raise e
  File "/Users/kanwals/miniconda/envs/cwltutorial/lib/python3.11/site-packages/libmambapy/__init__.py", line 4, in <module>
    from libmambapy.bindings import *  # noqa: F401,F403
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ImportError: dlopen(/Users/kanwals/miniconda/envs/cwltutorial/lib/python3.11/site-packages/libmambapy/bindings.cpython-311-darwin.so, 0x0002): Library not loaded: @rpath/libarchive.13.dylib
  Referenced from: <93863E94-4249-375D-BA9E-AF3A463FD1A0> /Users/kanwals/miniconda/envs/cwltutorial/lib/libmamba.2.0.0.dylib
  Reason: tried: '/Users/kanwals/miniconda/envs/cwltutorial/lib/libarchive.13.dylib' (no such file), '/Users/kanwals/miniconda/envs/cwltutorial/lib/python3.11/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/Users/kanwals/miniconda/envs/cwltutorial/lib/python3.11/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/Users/kanwals/miniconda/envs/cwltutorial/bin/../lib/libarchive.13.dylib' (no such file), '/Users/kanwals/miniconda/envs/cwltutorial/bin/../lib/libarchive.13.dylib' (no such file), '/usr/local/lib/libarchive.13.dylib' (no such file), '/usr/lib/libarchive.13.dylib' (no such file, not in dyld cache)

$ cwltool --print-dot rna_seq_workflow_2.cwl | dot -Tsvg > workflow_graph_2.svg
INFO /Users/kanwals/miniconda/envs/cwltutorial/bin/cwltool 3.1.20240404144621
INFO Resolved 'rna_seq_workflow_2.cwl' to 'file:///Users/kanwals/UMCCR/git/novice-tutorial-exercises/rna_seq_workflow_2.cwl'
WARNING Workflow checker warning:
rna_seq_workflow_2.cwl:51:11: Source 'alignment' of type ["File", {"type": "array", "items":
                              "File"}] may be incompatible
rna_seq_workflow_2.cwl:56:7:    with sink 'bam_sorted' of type "File"