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DeepIceDrain test environment for binder
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| LD_LIBRARY_PATH=${CONDA_PREFIX}/lib/ |
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| FROM buildpack-deps:bionic-scm@sha256:59661846ab0c581272f4b4688702617e6cc83ef1a9ae1cf918978126babbc858 AS base | |
| LABEL maintainer "https://github.com/weiji14" | |
| ENV LANG C.UTF-8 | |
| ENV LC_ALL C.UTF-8 | |
| # Initiate docker container with user 'jovyan' | |
| ARG NB_USER=jovyan | |
| ARG NB_UID=1000 | |
| ENV NB_USER ${NB_USER} | |
| ENV NB_UID ${NB_UID} | |
| ENV HOME /home/${NB_USER} | |
| RUN adduser --disabled-password \ | |
| --gecos "Default user" \ | |
| --uid ${NB_UID} \ | |
| ${NB_USER} | |
| # Setup conda | |
| ENV CONDA_DIR ${HOME}/.conda | |
| ENV NB_PYTHON_PREFIX ${CONDA_DIR} | |
| ENV MINICONDA_VERSION 4.7.10 | |
| RUN cd /tmp && \ | |
| wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \ | |
| echo "1c945f2b3335c7b2b15130b1b2dc5cf4 *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \ | |
| /bin/bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \ | |
| rm Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \ | |
| $CONDA_DIR/bin/conda config --system --prepend channels conda-forge && \ | |
| $CONDA_DIR/bin/conda config --system --set auto_update_conda false && \ | |
| $CONDA_DIR/bin/conda config --system --set show_channel_urls true && \ | |
| $CONDA_DIR/bin/conda clean --all --quiet --yes && \ | |
| $CONDA_DIR/bin/conda init --verbose | |
| # Setup $HOME directory with correct permissions | |
| USER root | |
| RUN chown -R ${NB_UID} ${HOME} | |
| USER ${NB_USER} | |
| WORKDIR ${HOME} | |
| # Change to interactive bash shell, so that `conda activate base` works | |
| SHELL ["/bin/bash", "-ic"] | |
| # Install dependencies in environment.yml file using conda | |
| COPY environment.yml ${HOME} | |
| RUN conda env update -n base -f environment.yml && \ | |
| conda clean --all --yes && \ | |
| conda list -n base | |
| # Install dependencies in Pipfile.lock using pipenv | |
| COPY Pipfile* ${HOME}/ | |
| RUN conda activate base && \ | |
| export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib && \ | |
| pipenv install --python ${CONDA_PREFIX}/bin/python --dev --deploy && \ | |
| rm --recursive ${HOME}/.cache/pip* && \ | |
| pipenv graph | |
| # Setup DeepBedMap virtual environment properly | |
| RUN conda activate base && \ | |
| pipenv run python -m ipykernel install --user --name deepicedrain && \ | |
| pipenv run jupyter kernelspec list --json | |
| # Copy remaining files to $HOME | |
| COPY --chown=1000:1000 . ${HOME} | |
| FROM base AS app | |
| # Run Jupyter Lab via pipenv in conda environment | |
| EXPOSE 8888 | |
| RUN echo -e '#!/bin/bash -i\nset -e\nconda activate\npipenv run "$@"' > .entrypoint.sh && \ | |
| chmod +x .entrypoint.sh | |
| ENTRYPOINT ["./.entrypoint.sh"] | |
| CMD ["jupyter", "lab", "--ip", "0.0.0.0"] |
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| name: deepicedrain | |
| channels: | |
| - conda-forge | |
| dependencies: | |
| - conda-forge::pip=19.2.3[md5=b475ca5f9afba8ab1203a413caa8e9ad] | |
| - conda-forge::python=3.7.3[md5=e9385633516bf38da68e983b4f8b9e2a] | |
| - pip: | |
| - pipenv==2018.11.26 |
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| [[source]] | |
| name = "pypi" | |
| url = "https://pypi.org/simple" | |
| verify_ssl = true | |
| [dev-packages] | |
| [packages] | |
| jupyterlab = "==1.2.0a0" | |
| [requires] | |
| python_version = "3.7" |
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| { | |
| "_meta": { | |
| "hash": { | |
| "sha256": "6850bb896187d0503ef4ceec58c656949908284d1e3eaed8e2320870b387308d" | |
| }, | |
| "pipfile-spec": 6, | |
| "requires": { | |
| "python_version": "3.7" | |
| }, | |
| "sources": [ | |
| { | |
| "name": "pypi", | |
| "url": "https://pypi.org/simple", | |
| "verify_ssl": true | |
| } | |
| ] | |
| }, | |
| "default": { | |
| "attrs": { | |
| "hashes": [ | |
| "sha256:ec20e7a4825331c1b5ebf261d111e16fa9612c1f7a5e1f884f12bd53a664dfd2", | |
| "sha256:f913492e1663d3c36f502e5e9ba6cd13cf19d7fab50aa13239e420fef95e1396" | |
| ], | |
| "version": "==19.2.0" | |
| }, | |
| "backcall": { | |
| "hashes": [ | |
| "sha256:38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4", | |
| "sha256:bbbf4b1e5cd2bdb08f915895b51081c041bac22394fdfcfdfbe9f14b77c08bf2" | |
| ], | |
| "version": "==0.1.0" | |
| }, | |
| "bleach": { | |
| "hashes": [ | |
| "sha256:213336e49e102af26d9cde77dd2d0397afabc5a6bf2fed985dc35b5d1e285a16", | |
| "sha256:3fdf7f77adcf649c9911387df51254b813185e32b2c6619f690b593a617e19fa" | |
| ], | |
| "version": "==3.1.0" | |
| }, | |
| "decorator": { | |
| "hashes": [ | |
| "sha256:86156361c50488b84a3f148056ea716ca587df2f0de1d34750d35c21312725de", | |
| "sha256:f069f3a01830ca754ba5258fde2278454a0b5b79e0d7f5c13b3b97e57d4acff6" | |
| ], | |
| "version": "==4.4.0" | |
| }, | |
| "defusedxml": { | |
| "hashes": [ | |
| "sha256:6687150770438374ab581bb7a1b327a847dd9c5749e396102de3fad4e8a3ef93", | |
| "sha256:f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5" | |
| ], | |
| "version": "==0.6.0" | |
| }, | |
| "entrypoints": { | |
| "hashes": [ | |
| "sha256:589f874b313739ad35be6e0cd7efde2a4e9b6fea91edcc34e58ecbb8dbe56d19", | |
| "sha256:c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451" | |
| ], | |
| "version": "==0.3" | |
| }, | |
| "ipykernel": { | |
| "hashes": [ | |
| "sha256:167c3ef08450f5e060b76c749905acb0e0fbef9365899377a4a1eae728864383", | |
| "sha256:b503913e0b4cce7ed2de965457dfb2edd633e8234161a60e23f2fe2161345d12" | |
| ], | |
| "version": "==5.1.2" | |
| }, | |
| "ipython": { | |
| "hashes": [ | |
| "sha256:c4ab005921641e40a68e405e286e7a1fcc464497e14d81b6914b4fd95e5dee9b", | |
| "sha256:dd76831f065f17bddd7eaa5c781f5ea32de5ef217592cf019e34043b56895aa1" | |
| ], | |
| "version": "==7.8.0" | |
| }, | |
| "ipython-genutils": { | |
| "hashes": [ | |
| "sha256:72dd37233799e619666c9f639a9da83c34013a73e8bbc79a7a6348d93c61fab8", | |
| "sha256:eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8" | |
| ], | |
| "version": "==0.2.0" | |
| }, | |
| "jedi": { | |
| "hashes": [ | |
| "sha256:786b6c3d80e2f06fd77162a07fed81b8baa22dde5d62896a790a331d6ac21a27", | |
| "sha256:ba859c74fa3c966a22f2aeebe1b74ee27e2a462f56d3f5f7ca4a59af61bfe42e" | |
| ], | |
| "version": "==0.15.1" | |
| }, | |
| "jinja2": { | |
| "hashes": [ | |
| "sha256:74320bb91f31270f9551d46522e33af46a80c3d619f4a4bf42b3164d30b5911f", | |
| "sha256:9fe95f19286cfefaa917656583d020be14e7859c6b0252588391e47db34527de" | |
| ], | |
| "version": "==2.10.3" | |
| }, | |
| "json5": { | |
| "hashes": [ | |
| "sha256:124b0f0da1ed2ff3bfe3a3e9b8630abd3c650852465cb52c15ef60b8e82a73b0", | |
| "sha256:32bd17e0553bf53927f6c29b6089f3a320c12897120a4bcfea76ea81c10b2d9c" | |
| ], | |
| "version": "==0.8.5" | |
| }, | |
| "jsonschema": { | |
| "hashes": [ | |
| "sha256:5f9c0a719ca2ce14c5de2fd350a64fd2d13e8539db29836a86adc990bb1a068f", | |
| "sha256:8d4a2b7b6c2237e0199c8ea1a6d3e05bf118e289ae2b9d7ba444182a2959560d" | |
| ], | |
| "version": "==3.0.2" | |
| }, | |
| "jupyter-client": { | |
| "hashes": [ | |
| "sha256:6a6d415c62179728f6d9295b37356d8f6833e9e01c2b6e1901dc555571f57b21", | |
| "sha256:f406f214f9daa92be110d5b83d62f3451ffc73d3522db7350f0554683533ab18" | |
| ], | |
| "version": "==5.3.3" | |
| }, | |
| "jupyter-core": { | |
| "hashes": [ | |
| "sha256:2c6e7c1e9f2ac45b5c2ceea5730bc9008d92fe59d0725eac57b04c0edfba24f7", | |
| "sha256:f4fa22d6cf25f34807c995f22d2923693575c70f02557bcbfbe59bd5ec8d8b84" | |
| ], | |
| "version": "==4.5.0" | |
| }, | |
| "jupyterlab": { | |
| "hashes": [ | |
| "sha256:124d71c5f9297e05e2fec6e105bb2f19aab63e9c3acb81d3826b7a1f8e5ce320", | |
| "sha256:d7c584d6fff7129728d9860755844fb02b0cedb4f36ec53163999c78fb757320" | |
| ], | |
| "index": "pypi", | |
| "version": "==1.2.0a0" | |
| }, | |
| "jupyterlab-server": { | |
| "hashes": [ | |
| "sha256:d0977527bfce6f47c782cb6bf79d2c949ebe3f22ac695fa000b730c671445dad", | |
| "sha256:d9c3bcf097f7ad8d8fd2f8d0c1e8a1b833671c02808e5f807088975495364447" | |
| ], | |
| "version": "==1.0.6" | |
| }, | |
| "markupsafe": { | |
| "hashes": [ | |
| "sha256:00bc623926325b26bb9605ae9eae8a215691f33cae5df11ca5424f06f2d1f473", | |
| "sha256:09027a7803a62ca78792ad89403b1b7a73a01c8cb65909cd876f7fcebd79b161", | |
| "sha256:09c4b7f37d6c648cb13f9230d847adf22f8171b1ccc4d5682398e77f40309235", | |
| "sha256:1027c282dad077d0bae18be6794e6b6b8c91d58ed8a8d89a89d59693b9131db5", | |
| "sha256:24982cc2533820871eba85ba648cd53d8623687ff11cbb805be4ff7b4c971aff", | |
| "sha256:29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b", | |
| "sha256:43a55c2930bbc139570ac2452adf3d70cdbb3cfe5912c71cdce1c2c6bbd9c5d1", | |
| "sha256:46c99d2de99945ec5cb54f23c8cd5689f6d7177305ebff350a58ce5f8de1669e", | |
| "sha256:500d4957e52ddc3351cabf489e79c91c17f6e0899158447047588650b5e69183", | |
| "sha256:535f6fc4d397c1563d08b88e485c3496cf5784e927af890fb3c3aac7f933ec66", | |
| "sha256:62fe6c95e3ec8a7fad637b7f3d372c15ec1caa01ab47926cfdf7a75b40e0eac1", | |
| "sha256:6dd73240d2af64df90aa7c4e7481e23825ea70af4b4922f8ede5b9e35f78a3b1", | |
| "sha256:717ba8fe3ae9cc0006d7c451f0bb265ee07739daf76355d06366154ee68d221e", | |
| "sha256:79855e1c5b8da654cf486b830bd42c06e8780cea587384cf6545b7d9ac013a0b", | |
| "sha256:7c1699dfe0cf8ff607dbdcc1e9b9af1755371f92a68f706051cc8c37d447c905", | |
| "sha256:88e5fcfb52ee7b911e8bb6d6aa2fd21fbecc674eadd44118a9cc3863f938e735", | |
| "sha256:8defac2f2ccd6805ebf65f5eeb132adcf2ab57aa11fdf4c0dd5169a004710e7d", | |
| "sha256:98c7086708b163d425c67c7a91bad6e466bb99d797aa64f965e9d25c12111a5e", | |
| "sha256:9add70b36c5666a2ed02b43b335fe19002ee5235efd4b8a89bfcf9005bebac0d", | |
| "sha256:9bf40443012702a1d2070043cb6291650a0841ece432556f784f004937f0f32c", | |
| "sha256:ade5e387d2ad0d7ebf59146cc00c8044acbd863725f887353a10df825fc8ae21", | |
| "sha256:b00c1de48212e4cc9603895652c5c410df699856a2853135b3967591e4beebc2", | |
| "sha256:b1282f8c00509d99fef04d8ba936b156d419be841854fe901d8ae224c59f0be5", | |
| "sha256:b2051432115498d3562c084a49bba65d97cf251f5a331c64a12ee7e04dacc51b", | |
| "sha256:ba59edeaa2fc6114428f1637ffff42da1e311e29382d81b339c1817d37ec93c6", | |
| "sha256:c8716a48d94b06bb3b2524c2b77e055fb313aeb4ea620c8dd03a105574ba704f", | |
| "sha256:cd5df75523866410809ca100dc9681e301e3c27567cf498077e8551b6d20e42f", | |
| "sha256:e249096428b3ae81b08327a63a485ad0878de3fb939049038579ac0ef61e17e7" | |
| ], | |
| "version": "==1.1.1" | |
| }, | |
| "mistune": { | |
| "hashes": [ | |
| "sha256:59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e", | |
| "sha256:88a1051873018da288eee8538d476dffe1262495144b33ecb586c4ab266bb8d4" | |
| ], | |
| "version": "==0.8.4" | |
| }, | |
| "nbconvert": { | |
| "hashes": [ | |
| "sha256:427a468ec26e7d68a529b95f578d5cbf018cb4c1f889e897681c2b6d11897695", | |
| "sha256:48d3c342057a2cf21e8df820d49ff27ab9f25fc72b8f15606bd47967333b2709" | |
| ], | |
| "version": "==5.6.0" | |
| }, | |
| "nbformat": { | |
| "hashes": [ | |
| "sha256:b9a0dbdbd45bb034f4f8893cafd6f652ea08c8c1674ba83f2dc55d3955743b0b", | |
| "sha256:f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402" | |
| ], | |
| "version": "==4.4.0" | |
| }, | |
| "notebook": { | |
| "hashes": [ | |
| "sha256:660976fe4fe45c7aa55e04bf4bccb9f9566749ff637e9020af3422f9921f9a5d", | |
| "sha256:b0a290f5cc7792d50a21bec62b3c221dd820bf00efa916ce9aeec4b5354bde20" | |
| ], | |
| "version": "==6.0.1" | |
| }, | |
| "pandocfilters": { | |
| "hashes": [ | |
| "sha256:b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9" | |
| ], | |
| "version": "==1.4.2" | |
| }, | |
| "parso": { | |
| "hashes": [ | |
| "sha256:63854233e1fadb5da97f2744b6b24346d2750b85965e7e399bec1620232797dc", | |
| "sha256:666b0ee4a7a1220f65d367617f2cd3ffddff3e205f3f16a0284df30e774c2a9c" | |
| ], | |
| "version": "==0.5.1" | |
| }, | |
| "pexpect": { | |
| "hashes": [ | |
| "sha256:2094eefdfcf37a1fdbfb9aa090862c1a4878e5c7e0e7e7088bdb511c558e5cd1", | |
| "sha256:9e2c1fd0e6ee3a49b28f95d4b33bc389c89b20af6a1255906e90ff1262ce62eb" | |
| ], | |
| "markers": "sys_platform != 'win32'", | |
| "version": "==4.7.0" | |
| }, | |
| "pickleshare": { | |
| "hashes": [ | |
| "sha256:87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca", | |
| "sha256:9649af414d74d4df115d5d718f82acb59c9d418196b7b4290ed47a12ce62df56" | |
| ], | |
| "version": "==0.7.5" | |
| }, | |
| "prometheus-client": { | |
| "hashes": [ | |
| "sha256:71cd24a2b3eb335cb800c7159f423df1bd4dcd5171b234be15e3f31ec9f622da" | |
| ], | |
| "version": "==0.7.1" | |
| }, | |
| "prompt-toolkit": { | |
| "hashes": [ | |
| "sha256:46642344ce457641f28fc9d1c9ca939b63dadf8df128b86f1b9860e59c73a5e4", | |
| "sha256:e7f8af9e3d70f514373bf41aa51bc33af12a6db3f71461ea47fea985defb2c31", | |
| "sha256:f15af68f66e664eaa559d4ac8a928111eebd5feda0c11738b5998045224829db" | |
| ], | |
| "version": "==2.0.10" | |
| }, | |
| "ptyprocess": { | |
| "hashes": [ | |
| "sha256:923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0", | |
| "sha256:d7cc528d76e76342423ca640335bd3633420dc1366f258cb31d05e865ef5ca1f" | |
| ], | |
| "markers": "os_name != 'nt'", | |
| "version": "==0.6.0" | |
| }, | |
| "pygments": { | |
| "hashes": [ | |
| "sha256:71e430bc85c88a430f000ac1d9b331d2407f681d6f6aec95e8bcfbc3df5b0127", | |
| "sha256:881c4c157e45f30af185c1ffe8d549d48ac9127433f2c380c24b84572ad66297" | |
| ], | |
| "version": "==2.4.2" | |
| }, | |
| "pyrsistent": { | |
| "hashes": [ | |
| "sha256:34b47fa169d6006b32e99d4b3c4031f155e6e68ebcc107d6454852e8e0ee6533" | |
| ], | |
| "version": "==0.15.4" | |
| }, | |
| "python-dateutil": { | |
| "hashes": [ | |
| "sha256:7e6584c74aeed623791615e26efd690f29817a27c73085b78e4bad02493df2fb", | |
| "sha256:c89805f6f4d64db21ed966fda138f8a5ed7a4fdbc1a8ee329ce1b74e3c74da9e" | |
| ], | |
| "version": "==2.8.0" | |
| }, | |
| "pyzmq": { | |
| "hashes": [ | |
| "sha256:01636e95a88d60118479041c6aaaaf5419c6485b7b1d37c9c4dd424b7b9f1121", | |
| "sha256:021dba0d1436516092c624359e5da51472b11ba8edffa334218912f7e8b65467", | |
| "sha256:0463bd941b6aead494d4035f7eebd70035293dd6caf8425993e85ad41de13fa3", | |
| "sha256:05fd51edd81eed798fccafdd49c936b6c166ffae7b32482e4d6d6a2e196af4e6", | |
| "sha256:1fadc8fbdf3d22753c36d4172169d184ee6654f8d6539e7af25029643363c490", | |
| "sha256:22efa0596cf245a78a99060fe5682c4cd00c58bb7614271129215c889062db80", | |
| "sha256:260c70b7c018905ec3659d0f04db735ac830fe27236e43b9dc0532cf7c9873ef", | |
| "sha256:2762c45e289732d4450406cedca35a9d4d71e449131ba2f491e0bf473e3d2ff2", | |
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https://binder.pangeo.io/v2/gist/weiji14/b9855537233c50af7710c4cb7726c448/master