Closed le-ander closed 4 years ago
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
this has been fixed in 4bf21a3eea1bce43516c55d4f8f9677e6816b3d8
Hi Anna,
when importing episcanpy 0.1.8, I get the following error:
Once I manually install pysam, this error disappears. I guess pysam should be added to the requirements file of episcanpy.