diff --git a/Dockerfile b/Dockerfile index 2b70c668727907c03dd0ce1986317acd33e89ce1..58108c0551d6629db7417388457d6c61cd828549 100644 --- a/Dockerfile +++ b/Dockerfile @@ -42,7 +42,7 @@ RUN useradd -ms /bin/bash clarkad #ENV QT_QPA_PLATFORM=xcb #ENV QT_PLUGIN_PATH=/usr/lib/x86_64-linux-gnu/qt5/plugins -RUN conda create -c conda-forge -n spyder-env spyder numpy scipy pandas matplotlib sympy cython +RUN conda create -y -c conda-forge -n spyder-env spyder numpy scipy pandas matplotlib sympy cython # Ensure conda is initialized in every new shell #RUN echo "source /opt/conda/etc/profile.d/conda.sh" >> /opt/.bashrc @@ -71,7 +71,7 @@ RUN conda create -c conda-forge -n spyder-env spyder numpy scipy pandas matplotl #RUN echo "conda activate cellxgene" >> /opt/.bashrc ADD cxg_env.yml /tmp/cxg_env.yml -RUN conda env create -f /tmp/cxg_env.yml +RUN conda env create -y -f /tmp/cxg_env.yml SHELL ["bash"] ENTRYPOINT [ "conda", "run", "--no-capture-output", "-n", "spyder-env", "spyder" ] \ No newline at end of file diff --git a/cxg_env.yml b/cxg_env.yml index aecc6e19aee254f35a7ec3ca58bb1b0606225d7b..383137f674b47f73b4995df338e117a928ab1c67 100644 --- a/cxg_env.yml +++ b/cxg_env.yml @@ -1,30 +1,58 @@ -name: cellxgene +name: cellxgene channels: - conda-forge - defaults dependencies: - _libgcc_mutex=0.1=main - _openmp_mutex=5.1=1_gnu + - backcall=0.2.0=pyhd3eb1b0_0 - ca-certificates=2024.6.2=hbcca054_0 - certifi=2024.6.2=pyhd8ed1ab_0 + - cloudpickle=2.0.0=pyhd3eb1b0_0 + - debugpy=1.5.1=py37h295c915_0 + - decorator=5.1.1=pyhd3eb1b0_0 + - entrypoints=0.4=py37h06a4308_0 + - ipykernel=6.16.2=pyh210e3f2_0 + - ipython=7.31.1=py37h06a4308_1 + - jedi=0.18.1=py37h06a4308_1 + - jupyter_client=7.4.9=py37h06a4308_0 + - jupyter_core=4.11.2=py37h06a4308_0 - ld_impl_linux-64=2.38=h1181459_1 - libffi=3.4.4=h6a678d5_1 - libgcc-ng=11.2.0=h1234567_1 - libgomp=11.2.0=h1234567_1 - libnsl=2.0.0=h7f98852_0 + - libsodium=1.0.18=h7b6447c_0 - libstdcxx-ng=11.2.0=h1234567_1 + - matplotlib-inline=0.1.6=py37h06a4308_0 - ncurses=6.4=h6a678d5_0 + - nest-asyncio=1.5.6=py37h06a4308_0 - openssl=1.1.1w=h7f8727e_0 - parallel=20240322=ha770c72_0 + - parso=0.8.3=pyhd3eb1b0_0 - perl=5.32.1=2_h7f98852_perl5 + - pexpect=4.8.0=pyhd3eb1b0_3 + - pickleshare=0.7.5=pyhd3eb1b0_1003 - pip=22.3.1=py37h06a4308_0 + - prompt-toolkit=3.0.36=py37h06a4308_0 + - psutil=5.9.0=py37h5eee18b_0 + - ptyprocess=0.7.0=pyhd3eb1b0_2 + - pygments=2.11.2=pyhd3eb1b0_0 - python=3.7.16=h7a1cb2a_0 + - pyzmq=23.2.0=py37h6a678d5_0 - readline=8.2=h5eee18b_0 - setuptools=65.6.3=py37h06a4308_0 + - six=1.16.0=pyhd3eb1b0_1 + - spyder-kernels=2.4.3=unix_pyhd8ed1ab_0 - sqlite=3.45.3=h5eee18b_0 - tk=8.6.14=h39e8969_0 + - tornado=6.2=py37h5eee18b_0 + - traitlets=5.7.1=py37h06a4308_0 + - wcwidth=0.2.5=pyhd3eb1b0_0 - wheel=0.38.4=py37h06a4308_0 + - wurlitzer=3.0.2=py37h06a4308_0 - xz=5.4.6=h5eee18b_1 + - zeromq=4.3.5=h6a678d5_0 - zlib=1.2.13=h5eee18b_1 - pip: - aniso8601==9.0.1 @@ -65,9 +93,9 @@ dependencies: - s3fs==0.4.2 - s3transfer==0.8.2 - scipy==1.7.3 - - six==1.16.0 - typing-extensions==4.7.1 - urllib3==1.26.19 - werkzeug==2.2.3 - zipp==3.15.0 - - zstandard==0.21.0 \ No newline at end of file + - zstandard==0.21.0 +prefix: /home/mdefende/.conda/envs/cellxgene