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sanger-pathogens / pymummer

Python3 module for running MUMmer and reading the output
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Python 3 pip installation failing #35

Open zmunro opened 3 years ago

zmunro commented 3 years ago

I have tried running installation with python3.6, 3.7, and 3.8 and I get a similar error message with each:

$ python3.6 -m pip install pymummer
Collecting pymummer
  Cache entry deserialization failed, entry ignored
  Cache entry deserialization failed, entry ignored
  Downloading https://files.pythonhosted.org/packages/9f/a4/78890f48a84be3d4733262327da70220be8e11147c7d58b87ea979a0f866/pymummer-0.11.0.tar.gz
    Complete output from command python setup.py egg_info:
    Checking MUMmer programs found in path:
       NOT FOUND        nucmer
       NOT FOUND        show-coords
       NOT FOUND        show-snps
       NOT FOUND        delta-filter
    Cannot install because some programs from the MUMer package not found.

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-ha4k5x9b/pymummer

Is there a fix for this available?

ghost commented 2 years ago

I don't know if this has changed, but the programs are now named (as of mummer 4.0rc1) mummer-nucmer, mummer-show-coords, etc. So, in setup.py, you need you change

required_progs = ['nucmer', 'show-coords', 'show-snps', 'delta-filter']

with this

required_progs = ['mummer-nucmer', 'mummer-show-coords', 'mummer-show-snps', 'mummer-delta-filter']

Now python setup.py test should say it did detect mummer, and can be installed.