running in Colab

[erfanhamdi]

Do you have any suggestion on how I can run it on colab? I am currently getting this error while running run_amp.py :

Traceback (most recent call last):
  File "run_amp.py", line 17, in <module>
    from lib.oracle_wrapper import get_oracle
  File "/content/drive/.shortcut-targets-by-id/1OJuMbwiWEwoAuUV13UWschS1lo8xwvQc/aptamer_generation/BioSeq-GFN-AL/lib/oracle_wrapper.py", line 3, in <module>
    from clamp_common_eval.defaults import get_test_oracle
  File "/content/drive/.shortcut-targets-by-id/1OJuMbwiWEwoAuUV13UWschS1lo8xwvQc/aptamer_generation/BioSeq-GFN-AL/clamp-gen-data/clamp_common_eval/defaults.py", line 12, in <module>
    from .oracles.proto_dist import MedioidDistanceOracle
  File "/content/drive/.shortcut-targets-by-id/1OJuMbwiWEwoAuUV13UWschS1lo8xwvQc/aptamer_generation/BioSeq-GFN-AL/clamp-gen-data/clamp_common_eval/oracles/proto_dist.py", line 123, in <module>
    class MedioidDistanceOracle(Oracle):
  File "/content/drive/.shortcut-targets-by-id/1OJuMbwiWEwoAuUV13UWschS1lo8xwvQc/aptamer_generation/BioSeq-GFN-AL/clamp-gen-data/clamp_common_eval/oracles/proto_dist.py", line 139, in MedioidDistanceOracle
    base_path=f"/dev/shm/{os.environ['USER']}/clamp/",
  File "/usr/lib/python3.8/os.py", line 675, in __getitem__
    raise KeyError(key) from None
KeyError: 'USER'

[MJ10]

Apologies for the late response. You can fix this by adding %env USER=xyz at the beginning of your notebook. It doesn't really make a difference since that class is not used in the code

[W-OK-E]

@erfanhamdi Were you able to run the whole thing in Colab? Can you please provide the steps that you took?