Dependencies missing from setup.py?

[holtgrewe]

pip install sv2 gives an error because Cython and numpy are missing.

[holtgrewe]

Also, specifying the dependency bedtools would be useful.

[dantaki]

I think pybedtools will install bedtools if it cannot find the executable in the environment path. Not sure, will fix this with the next update of SV2. Thanks for all your contributions.

[dantaki]

I can't replicate the issue, I did a clean pip install sv2 in a new conda environment

(base) bucephalus@bucephalus:~$ conda activate py2test
(py2test) bucephalus@bucephalus:~$ pip install sv2
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting sv2
Collecting cython (from sv2)
  Downloading https://files.pythonhosted.org/packages/38/d4/b8aaae645d1d33dfca8f95018fbcafdf5a882b80693a34165ff0b5c26aba/Cython-0.29.10-cp27-cp27mu-manylinux1_x86_64.whl (2.0MB)
     |████████████████████████████████| 2.0MB 10.1MB/s 
Collecting pybedtools (from sv2)
Collecting pysam>=0.9 (from sv2)
  Using cached https://files.pythonhosted.org/packages/0f/bd/f5ab828a9ff45a6ca14d5ea2a3580f720134052db258cd7ef929a4ed1d7a/pysam-0.15.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting scikit-learn>=0.19 (from sv2)
  Downloading https://files.pythonhosted.org/packages/f7/bb/52a01390c1dbb2c65d3072bc687271aa9ddf6964141ce7e03304820138f4/scikit_learn-0.20.3-cp27-cp27mu-manylinux1_x86_64.whl (5.5MB)
     |████████████████████████████████| 5.5MB 40.7MB/s 
Collecting pandas (from sv2)
  Downloading https://files.pythonhosted.org/packages/db/83/7d4008ffc2988066ff37f6a0bb6d7b60822367dcb36ba5e39aa7801fda54/pandas-0.24.2-cp27-cp27mu-manylinux1_x86_64.whl (10.1MB)
     |████████████████████████████████| 10.1MB 39.6MB/s 
Collecting wget (from sv2)
Collecting numpy (from sv2)
  Downloading https://files.pythonhosted.org/packages/1f/c7/198496417c9c2f6226616cff7dedf2115a4f4d0276613bab842ec8ac1e23/numpy-1.16.4-cp27-cp27mu-manylinux1_x86_64.whl (17.0MB)
     |████████████████████████████████| 17.0MB 40.0MB/s 
Collecting six (from pybedtools->sv2)
  Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting scipy>=0.13.3 (from scikit-learn>=0.19->sv2)
  Downloading https://files.pythonhosted.org/packages/1d/f6/7c16d60aeb3694e5611976cb4f1eaf1c6b7f1e7c55771d691013405a02ea/scipy-1.2.2-cp27-cp27mu-manylinux1_x86_64.whl (24.8MB)
     |████████████████████████████████| 24.8MB 44.5MB/s 
Collecting pytz>=2011k (from pandas->sv2)
  Downloading https://files.pythonhosted.org/packages/3d/73/fe30c2daaaa0713420d0382b16fbb761409f532c56bdcc514bf7b6262bb6/pytz-2019.1-py2.py3-none-any.whl (510kB)
     |████████████████████████████████| 512kB 31.1MB/s 
Collecting python-dateutil>=2.5.0 (from pandas->sv2)
  Downloading https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl (226kB)
     |████████████████████████████████| 235kB 26.7MB/s 
Installing collected packages: cython, six, pysam, pybedtools, numpy, scipy, scikit-learn, pytz, python-dateutil, pandas, wget, sv2
Successfully installed cython-0.29.10 numpy-1.16.4 pandas-0.24.2 pybedtools-0.8.0 pysam-0.15.2 python-dateutil-2.8.0 pytz-2019.1 scikit-learn-0.20.3 scipy-1.2.2 six-1.12.0 sv2-1.4.3.4 wget-3.2

[dantaki]

Not sure how to include a local bedtools install without evoking conda. Any suggestions?