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openvax / topiary

Predict mutated T-cell epitopes from sequencing data
Apache License 2.0
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Issue locating NetMHCpan #77

Closed ARChakravarthy closed 6 years ago

ARChakravarthy commented 6 years ago

Hi there,

I am trying to call neoepitopes using a locally installed version of topiary and NetMHCpan, and keep running into this error

Traceback (most recent call last): File "/usr/local/bin/topiary", line 58, in main(args) File "/usr/local/bin/topiary", line 43, in main epitopes = predict_epitopes_from_args(args) File "/usr/local/lib/python2.7/dist-packages/topiary/predict_epitopes.py", line 273, in predict_epitopes_from_args mhc_model = mhc_binding_predictor_from_args(args) File "/usr/local/lib/python2.7/dist-packages/mhctools/cli/args.py", line 150, in mhc_binding_predictor_from_args return mhc_class(**kwargs) File "/usr/local/lib/python2.7/dist-packages/mhctools/netmhc_pan.py", line 43, in NetMHCpan stderr=devnull) File "/usr/lib/python2.7/subprocess.py", line 573, in check_output raise CalledProcessError(retcode, cmd, output=output) subprocess.CalledProcessError: Command '['netMHCpan', '--version', '_MHCTOOLS_VERSION_SNIFFING']' returned non-zero exit status 1

The netMHCpan install on my computer is version 3.0, and interestingly netMHCpan by itself has issues calling the version command internally (although I can do it externally using an echo command)

ARChakravarthy commented 6 years ago

I figured out there was an issue with my path to NetMHCpan