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PNNL-CompBio / coderdata

Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.
BSD 3-Clause "New" or "Revised" License
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cptac samples failing when running from build_all.py #172

Closed jjacobson95 closed 3 weeks ago

jjacobson95 commented 3 weeks ago

EC2 Instance Information: · Amazon Linux 2 AMI (HVM) – Kernel 5.10, SSD Volume Type · SSD Volume · Architecture: 64-bit x86 · Instance type: t2.large (8gb mem) · Storage 1 x 30GB gp2 · Python3.10 Installed

Error:

running...cptac samples
['docker', 'run', '-v', '/home/ec2-user/coderdata/local/:/tmp/', '-e', 'SYNAPSE_AUTH_TOKEN=[my_token]', '--platform=linux/amd64', 'cptac', 'sh', 'build_samples.sh', '/tmp/mpnst_samples.csv']
Traceback (most recent call last):
  File "/app/getCptacData.py", line 6, in <module>
    import cptac
  File "/opt/venv/lib/python3.11/site-packages/cptac/__init__.py", line 32, in <module>
    from cptac.cancers.brca import Brca
  File "/opt/venv/lib/python3.11/site-packages/cptac/cancers/brca.py", line 16, in <module>
    from cptac.cancers.broad.broadbrca import BroadBrca
  File "/opt/venv/lib/python3.11/site-packages/cptac/cancers/broad/broadbrca.py", line 14, in <module>
    from pyranges import read_gtf
  File "/opt/venv/lib/python3.11/site-packages/pyranges/__init__.py", line 6, in <module>
    from pyranges import orfs, seqs, stats  # noqa: F401
  File "/opt/venv/lib/python3.11/site-packages/pyranges/orfs.py", line 1, in <module>
    from pyranges.ext.orfs import calculate_frame, extend_orfs  # noqa: F401
  File "/opt/venv/lib/python3.11/site-packages/pyranges/ext/orfs.py", line 11, in <module>
    from pyranges.core.names import (
  File "/opt/venv/lib/python3.11/site-packages/pyranges/core/names.py", line 131
    class UnaryOperation[T: "RangeFrame"](Protocol):
                        ^
SyntaxError: invalid syntax
cptac samples file failed
sgosline commented 3 weeks ago

This is again the cptac build that i filed. In the NCI60 branch i moved the cptac samples to the last element so it doesnt' break everything, and for some reason it seems to be working there (I did some version updates on pandas/cptac, as the pandas is what's causing the problem).