Episcanpy 0.1.8 should require pysam

[le-ander]

Hi Anna,

when importing episcanpy 0.1.8, I get the following error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/app/python37/lib/python3.7/site-packages/episcanpy/__init__.py", line 25, in <module>
    from . import count_matrix as ct
  File "/app/python37/lib/python3.7/site-packages/episcanpy/count_matrix/__init__.py", line 6, in <module>
    from ..count_matrix._bld_atac_mtx import bld_mtx_fly
  File "/app/python37/lib/python3.7/site-packages/episcanpy/count_matrix/_bld_atac_mtx.py", line 5, in <module>
    import pysam
ModuleNotFoundError: No module named 'pysam'

Once I manually install pysam, this error disappears. I guess pysam should be added to the requirements file of episcanpy.

[kridsadakorn]

If you want to install the version on Github, this configuration may help

RUN conda install -y \ conda==4.7.10 \ && conda clean -ya RUN conda install -y --channel=bioconda --channel=conda-forge \ jupyter==1.0.0 \ louvain==0.6.1 \ numba==0.45.0 \ python-igraph==0.7.1.post7 \ scipy==1.4.1 \ seaborn==0.9.0 \ statsmodels==0.10.0 \ && conda clean -ya

RUN pip install -U --no-cache-dir --upgrade-strategy=only-if-needed \ cmake==3.13.3 \ matplotlib==3.1.0 \ multicoretsne==0.1 \ numpy==1.16.4 \ pandas==0.24.2 \ pysam==0.15.3 \ scanpy==1.4.4.post1 \ scikit-learn==0.21.2 \ -e git+https://github.com/colomemaria/epiScanpy#egg=2bd1a9e235693251adc60d73ac5fe6abf76729fc

[le-ander]

this has been fixed in 4bf21a3eea1bce43516c55d4f8f9677e6816b3d8