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hardingnj / xpclr

Code to compute the XP-CLR statistic to infer natural selection
MIT License
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Issue: The 'xpclr==1.1.2' distribution was not found and is required by the application #74

Open ricebrian opened 2 years ago

ricebrian commented 2 years ago

Hi @hardingnj Thank you for maintaining a software to easily run xpclr. I am running into an issue my first time trying to run the program. I am running on Mac BigSlur. My test inputs are below.

xpclr --out Chr1.txt --format VCF --input haiti_global_all_together.vcf --samplesA 296taxa_haitan.txt --samplesB global_diversity_taxa.txt --rrate 1.71312383957495e-06 --chr 1 --ld 0.95 --maxsnps 200 --minsnps 10 --size 200 --start 1714 --stop 80871376 --step 50

I get the error/traceback messages:

Traceback (most recent call last): File "/usr/local/bin/xpclr", line 4, in import('pkg_resources').run_script('xpclr==1.1.2', 'xpclr') File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/init.py", line 3241, in @_call_aside File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/init.py", line 3225, in _call_aside f(*args, **kwargs) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/init.py", line 3254, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/init.py", line 583, in _build_master ws.require(requires) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/init.py", line 900, in require needed = self.resolve(parse_requirements(requirements)) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/init.py", line 786, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'xpclr==1.1.2' distribution was not found and is required by the application

My best guess is I am missing a dependency or an update version of a package on BigSlur is giving issues. Do you have any clue?

Thanks, Brian

hardingnj commented 2 years ago

Thanks. I think this is a python 2/3 issue. I'm not (knowingly) supporting 2. But there is some conda dependency weirdness that means currently 2 is installed via conda install xpclr.

This is related to https://github.com/hardingnj/xpclr/issues/65 possibly.

Essentially the dependency list needs resolving/updating. Sorry I can't be more help at the moment.

ricebrian commented 2 years ago

Thanks for the reply. What version of python is it optimized for? I can try switching to that version

hardingnj commented 2 years ago

>3.4. But there is some dependency conflict somewhere that makes this not possible to install (at least via the simplest path), and rolls back to 2.x

hardingnj commented 2 years ago

I spent some time a while ago attempting to debug this. I don't have time though at the moment unfortunately.

If you can verify it is python 2 getting installed via conda install xpclr might be worth posting a message on the bioconda repo.

ricebrian commented 2 years ago

I just ended up installing via python as it works fine on BigSlur