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mcmero / SVclone

A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.
BSD 3-Clause "New" or "Revised" License
40 stars 10 forks source link

Docker Version #1

Closed xtmgah closed 6 years ago

xtmgah commented 6 years ago

Hello:

We are trying to using SVclone do some analyses. thanks for developing this software, it's very useful. Do you have any docker version? We have some issue to install it. it's have the following error, do you have any idea? Thanks.

zhangt8@cn3241:/data/zhangt8/Ref/SVclone/SVclone$ SVclone.py -h Traceback (most recent call last): File "/usr/local/apps/svclone/0.2.2-13-ge402c3f/SVclone.py", line 7, in from SVclone import run_filter File "/usr/local/apps/svclone/0.2.2-13-ge402c3f/SVclone/run_filter.py", line 15, in from . import run_clus File "/usr/local/apps/svclone/0.2.2-13-ge402c3f/SVclone/run_clus.py", line 25, in from . import cluster File "/usr/local/apps/svclone/0.2.2-13-ge402c3f/SVclone/cluster.py", line 8, in from sklearn.cluster import KMeans File "/home/zhangt8/.local/lib/python2.7/site-packages/sklearn/cluster/init.py", line 6, in from .spectral import spectral_clustering, SpectralClustering File "/home/zhangt8/.local/lib/python2.7/site-packages/sklearn/cluster/spectral.py", line 17, in from ..manifold import spectral_embedding File "/home/zhangt8/.local/lib/python2.7/site-packages/sklearn/manifold/init.py", line 8, in from .spectralembedding import SpectralEmbedding, spectral_embedding File "/home/zhangt8/.local/lib/python2.7/site-packages/sklearn/manifold/spectralembedding.py", line 12, in from scipy.sparse.linalg.eigen.lobpcg.lobpcg import symeig ImportError: cannot import name symeig

If you suspect this is an IPython bug, please report it at: https://github.com/ipython/ipython/issues or send an email to the mailing list at ipython-dev@python.org

You can print a more detailed traceback right now with "%tb", or use "%debug" to interactively debug it.

Extra-detailed tracebacks for bug-reporting purposes can be enabled via: %config Application.verbose_crash=True

mcmero commented 5 years ago

Thank you for reporting this and sorry about the late reply. The clustering code has changed significantly and no longer requires scikitlearn, so the bug you reported should no longer occur. We currently do not have a docker version, but will consider one for the future.