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jj-umn / galaxytools

Galaxy Tool wrappers
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latest update of optitype fails with an error #2

Open ksenia-krasheninnikova opened 3 years ago

ksenia-krasheninnikova commented 3 years ago

Hello,

Optitype package (toolshed.g2.bx.psu.edu/repos/jjohnson/optitype/optitype/1.3.2) was installed into a local galaxy server from the toolshed. It was run on the paired-end data in the DNA mode and failed with the following error:

Traceback (most recent call last): File "/home/ksenia/melanoma/galaxy/galaxy/database/dependencies/_conda/envs/optitype@1.3.2/bin/OptiTypePipeline.py", line 129, in from model import OptiType File "/home/ksenia/melanoma/galaxy/galaxy/database/dependencies/_conda/envs/__optitype@1.3.2/share/optitype-1.3.2-3/model.py", line 19, in from pyomo.environ import ConcreteModel, Set, Param, Var, Binary, Objective, Constraint, ConstraintList, maximize File "/home/ksenia/melanoma/galaxy/galaxy/database/dependencies/_conda/envs/optitype@1.3.2/lib/python2.7/site-packages/pyomo/environ/init.py", line 97, in _import_packages() File "/home/ksenia/melanoma/galaxy/galaxy/database/dependencies/_conda/envs/__optitype@1.3.2/lib/python2.7/site-packages/pyomo/environ/init.py", line 81, in _import_packages raise ImportError(msg) ImportError: pyomo.environ failed to import pyomo.core.plugins: Original ImportError: pyutilib.enum has been removed.

Python 3 now has an enum implementation in the standard library (also available for older Python versions as the third-party enum34 PyPI package) that supersedes this library. Traceback: File "/home/ksenia/melanoma/galaxy/galaxy/database/dependencies/_conda/envs/optitype@1.3.2/lib/python2.7/site-packages/pyomo/environ/init.py", line 69, in _import_packages _do_import(pname) File "/home/ksenia/melanoma/galaxy/galaxy/database/dependencies/_conda/envs/optitype@1.3.2/lib/python2.7/site-packages/pyomo/environ/init.py", line 19, in _do_import import(pkg_name, globals(), locals(), [], -1) File "/home/ksenia/melanoma/galaxy/galaxy/database/dependencies/_conda/envs/optitype@1.3.2/lib/python2.7/site-packages/pyomo/core/init.py", line 11, in from pyomo.core.expr import * File "/home/ksenia/melanoma/galaxy/galaxy/database/dependencies/_conda/envs/optitype@1.3.2/lib/python2.7/site-packages/pyomo/core/expr/init.py", line 36, in from .calculus.derivatives import differentiate File "/home/ksenia/melanoma/galaxy/galaxy/database/dependencies/_conda/envs/__optitype@1.3.2/lib/python2.7/site-packages/pyomo/core/expr/calculus/derivatives.py", line 3, in from pyutilib.enum import Enum File "/home/ksenia/melanoma/galaxy/galaxy/database/dependencies/_conda/envs/__optitype@1.3.2/lib/python2.7/site-packages/pyutilib/enum/init.py", line 18, in package) that supersedes this library.""")

A fix or possible solution would be most appreciated.

Thank you!

Best regards,

Ksenia

jj-umn commented 3 years ago

@ksenia-krasheninnikova Sorry, I haven't had the time to work on this issue. I hope to check on this in the next few weeks. We have a researcher at University of Minnesota that considers optitype results as more reliable than seqHLA for some patients.

ksenia-krasheninnikova commented 3 years ago

OK good to know. Thank you for this information. Looking forward to the updates.

jj-umn commented 3 years ago

@ksenia-krasheninnikova I've updated Optitype to use version 1.3.5 and that has fixed issues for me. Can you let me know if the newer version works for you? Thanks.