ResolvePackageNotFound: nupack=3.0.6

[alexlenail]

Hi,
I tried to do a fresh install from environment.yml on my M1 mac, but ran into a bug.

ResolvePackageNotFound:
  - nupack=3.0.6

I made the environment without nupack, and tried to install nupack subsequently, but got another error.

DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support

ERROR: Could not find a version that satisfies the requirement nupack==3.0.6 (from versions: none)
ERROR: No matching distribution found for nupack==3.0.6

nupack needed to be installed separately. I registered for an account at nupack.org, and downloaded and untarred nupack 3.0.6.

I did make in the root directory as is called for by the NUPACK 3.0 User Guide.

It appears that 3.0.6 has no python package, only executables. I added those executables to my $PATH.

I then ran structureCheck.py with the example file, with the same command as is in the README.

$ python OligoMiner/structureCheck.py -f OligoMiner/ExampleFiles/3_probes.bed -t 0.4
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NUPACK ERROR: could not run prob command with these inputs.
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NUPACK ERROR: could not run prob command with these inputs.
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NUPACK ERROR: could not run prob command with these inputs.
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NUPACK ERROR: could not run prob command with these inputs.
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NUPACK ERROR: could not run prob command with these inputs.
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NUPACK ERROR: could not run prob command with these inputs.
***********************************************************
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NUPACK ERROR: could not run prob command with these inputs.
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NUPACK ERROR: could not run prob command with these inputs.
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NUPACK ERROR: could not run prob command with these inputs.
***********************************************************
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NUPACK ERROR: could not run prob command with these inputs.
***********************************************************
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NUPACK ERROR: could not run prob command with these inputs.
***********************************************************
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NUPACK ERROR: could not run prob command with these inputs.
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structureCheck predicted that 0 of 12 / 0.0000% candidate probes are predicted to have a linear structure with p>0.4000 at 47C in 390 mM Na+ and 50% formamide
Program took 0.080418 seconds

[brianbeliveau]

Hi,

Unfortunately NUPACK is in the process of moving to a subscription-only model, and as a result conda/pypi support has been phased out. You will need to compile and valid a local install of NUPACK in order to run structureCheck.py

Please test the NUPACK executables using bash. They should work after successful compilation, provided they are in your path.

[JungnamChoLab]

Hi alexlenail,

You added those executables to your $PATH. But maybe you did not add NUPACKHOME path.
Please export NUPACKHOME=/path/to/nupack
Then test NUPACK by using: prob Enter sequence: Any sequence like AAAATT Enter structure: ......
If it worked then all will be fine.

Just sloved