mills-lab / vapor

Tool for the validation of structural genomic rearrangements using long read sequence data
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python dependencies #1

Closed calkan closed 7 years ago

calkan commented 7 years ago

./ vapor File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 829, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'sklearn' distribution was not found and is required by VaPoR

however: sudo apt install python-sklearn Reading package lists... Done Building dependency tree
Reading state information... Done python-sklearn is already the newest version (0.17.0-4). 0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.

sudo apt install python-sklearn-lib Reading package lists... Done Building dependency tree
Reading state information... Done python-sklearn-lib is already the newest version (0.17.0-4). 0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.

ls /usr/lib/python2.7/dist-packages/sklearn/ base.py cluster discriminant_analysis.py feature_selection isotonic.pyc lda.pyc multiclass.py pipeline.pyc setup.py base.pyc covariance discriminant_analysis.pyc gaussian_process _isotonic.x86_64-linux-gnu.so learning_curve.py multiclass.pyc preprocessing setup.pyc _build_utils.py cross_decomposition dummy.py grid_search.py kernel_approximation.py learning_curve.pyc naive_bayes.py qda.py svm _build_utils.pyc cross_validation.py dummy.pyc grid_search.pyc kernel_approximation.pyc linear_model naive_bayes.pyc qda.pyc tests calibration.py cross_validation.pyc ensemble init.py kernel_ridge.py manifold neighbors random_projection.py tree calibration.pyc datasets externals init.pyc kernel_ridge.pyc metrics neural_network random_projection.pyc utils __check_build decomposition feature_extraction isotonic.py lda.py mixture pipeline.py semi_supervised

calkan commented 7 years ago

poke @remills

xuefzhao commented 7 years ago

Hi,

can you first try 'pip install scikit-learn' to install sklearn, and then try vapor to see if the same problem still exits?

calkan commented 7 years ago

It worked after that, and a few updates and links. At least the help menu is printed now. And python is bullshit. @remills