python is working

docker/codabench_hadaca_final/Dockerfile

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+# FROM mambaorg/micromamba:1.5.8
+
+# # WORKDIR /app
+
+
+# COPY environment/environment-r.yml .
+
+# RUN micromamba env create -f environment-r.yml && micromamba clean --all --yes
+
+
+# SHELL ["micromamba", "run", "-n", "h3", "/bin/bash", "-c"]
+
+# RUN echo 'micromamba activate h3' >> ~/.bashrc
+
+# ENV PATH /opt/conda/bin:$PATH
+
+
+
+
+
+# FROM mambaorg/micromamba:1.5.8
+FROM mambaorg/micromamba:2.0.3
+RUN micromamba create -n h3_final
+RUN micromamba run -n h3_final micromamba install -y -c anaconda -c bioconda -c conda-forge -c r r-base snakemake=7.32.4 python=3.9 r-rmarkdown r-prettydoc r-seurat r-clue bioconductor-complexheatmap r-viridis r-magrittr r-dplyr r-nnls graphviz r-tictoc  graphviz python-kaleido tenacity plotly r-bisquerna r-extraDistr r-MASS r-EPIC r-BiocManager numpy pandas rpy2 r-infotheo r-combinat
+# RUN micromamba run -n h3_final pip install smgantt==0.0.5
+RUN micromamba clean --all --yes
+RUN echo 'micromamba activate h3_final' >> ~/.bashrc
+ENV PATH /opt/conda/bin:$PATH
+
+
+### Participants requested pacakges
+## Install R packages
+RUN micromamba run -n h3_final micromamba install -y -c bioconda -c conda-forge -c r r-nnls r-mixOmics r-RGCCA r-bigsnpr  r-NMF r-fastICA r-ggplot2  r-CCA r-FactoMineR r-seurat r-velocyto.R 
+#r-monocle3 r-RcppML 
+# r-JADE r-NNLM r-citcdf 
+#r-MAST r-scDD r-SigEMD 
+#r-DESingle r-SCDE r-D3E r-tidyverse r-data.table r-parallel 
+#r-ggrepel r-Seurat r-keras r-rstan r-bnlearn r-ranger r-randomForest r-tensorflow r-keras3 r-rethinking r-glmnet r-torch r-RSNNS r-caret r-rpart r-tree r-RWeka r-e1071 r-rgenoud r-kernlab r-DoubleML r-rminer r-mlr3 r-BART r-bartMachine r-BayesTree r-gbm r-elasticnet r-ctv r-ggpubr r-dplyr r-tidyr r-plotly r-consICA r-pheatmap r-SummarizedExperiment r-future r-devtools r-assertr r-assertthat
+
+## not installed : 
+# r-DESeq2 r-ProDenICA
+
+
+
+
+###pandas was not imported uplaoded correctly.  no numpy... wtf...
+
+## Intall Pyton packages
+# RUN micromamba run -n h3_final micromamba  install -y -c bioconda -c conda-forge pandas, matplotlib, stabilized-ica, numpy, scipy, scanpy, squidpy, anndata, seaborn, torch, torch_geometric, umap-learn, keras, os, libtorch, omicverse, ucdeconvolve, tensorflow,  inmoose, scikit-learn, statsmodels, nltk, request, xgboost, biopython, pytest, pandera, chardet, codecarbon, pyarrow, pytables, openpyxl, coverage, ruff, pyspark, networkx, MOWGLI
+
+
+SHELL ["micromamba", "run", "-n", "h3_final", "/bin/bash", "-c"]
+RUN Rscript -e 'install.packages( pkgs = "zip", repos = "https://cloud.r-project.org")'
+RUN Rscript  -e 'BiocManager::install("ComplexHeatmap")'
+RUN Rscript  -e 'BiocManager::install("Biobase")'
+
+ENTRYPOINT ["micromamba", "run", "-n", "h3_final"]
+
+
+
+USER root
+RUN apt-get update && apt-get install -y --fix-missing r-base 
+RUN apt-get update && apt-get upgrade -y && apt-get install -y gzip
+
+
+
+
+# # Python requirements
+# FROM debian:11.0
+
+# RUN apt update --fix-missing
+
+# # # Install anaconda
+# # RUN apt-get update --fix-missing && apt-get install -y wget bzip2 ca-certificates \
+# #     libglib2.0-0 libxext6 libsm6 libxrender1 \
+# #     git mercurial subversion
+# # RUN echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
+# #     wget --quiet https://repo.continuum.io/archive/Anaconda3-2022.05-Linux-x86_64.sh && \
+# #     /bin/bash /Anaconda3-2022.05-Linux-x86_64.sh -b -p /opt/conda && \
+# #     rm /Anaconda3-2022.05-Linux-x86_64.sh
+
+# # RUN apt-get install -y curl grep sed dpkg tini
+
+# ENV PATH /opt/conda/bin:$PATH
+# ENV R_LIBS=/usr/local/lib/R/site-library
+
+# # C#, R, etc. requirements
+# RUN apt-get update && apt-get install -y --fix-missing r-base 
+# #mono-runtime libgomp1 libc6
+
+# # Fix for 'xgboost' missing
+# # RUN conda install libgcc
+# #RUN conda install -c conda-forge tensorflow
+
+# # RUN echo "deb http://http.us.debian.org/debian/ testing non-free contrib main" > /etc/apt/sources.list && \
+# #     apt-get update 
+#     # apt-get -y -t testing install python3.9 python3-pip
+
+# RUN apt-get install gzip
+# RUN  apt-get -y install pandoc && apt-get clean && apt-get auto-clean && apt-get -y auto-remove
+
+# # RUN pip3 install \
+# #         theano==1.0.5 \
+# #         Cython==0.29.30 \
+# #         numpy==1.22.4 \
+# #         scipy==1.8.1 \
+# #         scikit-learn==1.1.1 \
+# #         pandas==1.4.2 \
+# #         pyyaml==6.0 \
+# #         imutils==0.5.4 \
+# #         numba==0.55.2 \
+# #         tensorflow==2.9.1
+
+
+# RUN  Rscript -e 'install.packages(pkgs = "BiocManager")'
+
+# RUN  Rscript -e 'BiocManager::install(pkgs = "Biobase")'
+# RUN  Rscript -e 'install.packages(pkgs = "zip")'
+# RUN Rscript -e 'install.packages(pkgs=c("utf8", "farver", "labeling", "munsell", "R6", "viridisLite", "fansi", "pillar", "pkgconfig", "cli", "glue", "lifecycle", "magrittr", "rlang", "stringi", "vctrs", "iterators", "gtable", "isoband", "scales", "tibble", "withr", "plyr", "Rcpp", "registry", "rngtools", "stringr", "digest", "gridBase", "colorspace", "RColorBrewer", "foreach", "doParallel", "ggplot2", "reshape2"))'
+# RUN Rscript -e 'install.packages(pkgs=c("fs", "rappdirs", "base64enc", "cachem", "fastmap", "memoise", "mime", "sass", "highr", "bslib", "evaluate", "fontawesome", "htmltools", "jquerylib", "jsonlite", "knitr", "tinytex", "xfun", "yaml"))'
+# RUN Rscript -e 'install.packages(pkgs=c( "combinat",  "rmarkdown", "clue","infotheo"))'
+
+# RUN  Rscript -e 'install.packages(pkgs = "NMF", repos = "https://cloud.r-project.org")'
+
+# RUN Rscript -e 'install.packages(pkgs=c( "bitops",  "caTools", "gplots","viridis"))'
+
+# COPY environment/requirements.txt .
+
+# RUN pip3 install --no-cache-dir -r requirements.txt
+

docker/codabench_hadaca_final/environment/environment-r.yml

@@ -0,0 +1,259 @@
+name: h3
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - _r-mutex=1.0.0=anacondar_1
+  - _sysroot_linux-64_curr_repodata_hack=3=haa98f57_10
+  - asttokens=2.4.1=pyhd8ed1ab_0
+  - binutils_impl_linux-64=2.38=h2a08ee3_1
+  - binutils_linux-64=2.38.0=hc2dff05_0
+  - blas=1.0=openblas
+  - bottleneck=1.3.7=py311hf4808d0_0
+  - bwidget=1.9.16=h9eba36c_0
+  - bzip2=1.0.8=h5eee18b_6
+  - c-ares=1.19.1=h5eee18b_0
+  - ca-certificates=2024.8.30=hbcca054_0
+  - cairo=1.16.0=hb05425b_5
+  - cffi=1.16.0=py311h5eee18b_1
+  - comm=0.2.2=pyhd8ed1ab_0
+  - curl=8.7.1=hdbd6064_0
+  - debugpy=1.6.7=py311h6a678d5_0
+  - decorator=5.1.1=pyhd8ed1ab_0
+  - exceptiongroup=1.2.2=pyhd8ed1ab_0
+  - executing=2.1.0=pyhd8ed1ab_0
+  - expat=2.6.2=h6a678d5_0
+  - fontconfig=2.14.1=h4c34cd2_2
+  - freetype=2.12.1=h4a9f257_0
+  - fribidi=1.0.10=h7b6447c_0
+  - gcc_impl_linux-64=11.2.0=h1234567_1
+  - gcc_linux-64=11.2.0=h5c386dc_0
+  - gfortran_impl_linux-64=11.2.0=h1234567_1
+  - gfortran_linux-64=11.2.0=hc2dff05_0
+  - glib=2.78.4=h6a678d5_0
+  - glib-tools=2.78.4=h6a678d5_0
+  - graphite2=1.3.14=h295c915_1
+  - gxx_impl_linux-64=11.2.0=h1234567_1
+  - gxx_linux-64=11.2.0=hc2dff05_0
+  - harfbuzz=4.3.0=hf52aaf7_2
+  - icu=73.1=h6a678d5_0
+  - importlib-metadata=8.4.0=pyha770c72_0
+  - importlib_metadata=8.4.0=hd8ed1ab_0
+  - ipykernel=6.29.5=pyh3099207_0
+  - ipython=8.27.0=pyh707e725_0
+  - jedi=0.19.1=pyhd8ed1ab_0
+  - jinja2=3.1.4=py311h06a4308_0
+  - jpeg=9e=h5eee18b_1
+  - jupyter_client=8.6.2=pyhd8ed1ab_0
+  - jupyter_core=5.7.2=py311h38be061_0
+  - kernel-headers_linux-64=3.10.0=h57e8cba_10
+  - krb5=1.20.1=h143b758_1
+  - ld_impl_linux-64=2.38=h1181459_1
+  - lerc=3.0=h295c915_0
+  - libcurl=8.7.1=h251f7ec_0
+  - libdeflate=1.17=h5eee18b_1
+  - libedit=3.1.20230828=h5eee18b_0
+  - libev=4.33=h7f8727e_1
+  - libffi=3.4.4=h6a678d5_1
+  - libgcc-devel_linux-64=11.2.0=h1234567_1
+  - libgcc-ng=14.1.0=h77fa898_0
+  - libgfortran-ng=11.2.0=h00389a5_1
+  - libgfortran5=11.2.0=h1234567_1
+  - libglib=2.78.4=hdc74915_0
+  - libgomp=14.1.0=h77fa898_0
+  - libiconv=1.16=h5eee18b_3
+  - libnghttp2=1.57.0=h2d74bed_0
+  - libopenblas=0.3.21=h043d6bf_0
+  - libpng=1.6.39=h5eee18b_0
+  - libsodium=1.0.18=h36c2ea0_1
+  - libssh2=1.11.0=h251f7ec_0
+  - libstdcxx-devel_linux-64=11.2.0=h1234567_1
+  - libstdcxx-ng=11.2.0=h1234567_1
+  - libtiff=4.5.1=h6a678d5_0
+  - libuuid=1.41.5=h5eee18b_0
+  - libwebp-base=1.3.2=h5eee18b_0
+  - libxcb=1.16=hd590300_0
+  - libxml2=2.10.4=hfdd30dd_2
+  - lz4-c=1.9.4=h6a678d5_1
+  - make=4.2.1=h1bed415_1
+  - markupsafe=2.1.3=py311h5eee18b_0
+  - matplotlib-inline=0.1.7=pyhd8ed1ab_0
+  - ncurses=6.4=h6a678d5_0
+  - nest-asyncio=1.6.0=pyhd8ed1ab_0
+  - numexpr=2.8.7=py311h812550d_0
+  - numpy=1.26.4=py311h24aa872_0
+  - numpy-base=1.26.4=py311hbfb1bba_0
+  - openssl=3.3.1=hb9d3cd8_3
+  - packaging=24.1=pyhd8ed1ab_0
+  - pandas=2.2.2=py311ha02d727_0
+  - pandoc=2.12=h06a4308_3
+  - pango=1.50.7=h05da053_0
+  - parso=0.8.4=pyhd8ed1ab_0
+  - pcre2=10.42=hebb0a14_1
+  - pexpect=4.9.0=pyhd8ed1ab_0
+  - pickleshare=0.7.5=py_1003
+  - pip=24.0=py311h06a4308_0
+  - pixman=0.40.0=h7f8727e_1
+  - platformdirs=4.2.2=pyhd8ed1ab_0
+  - prompt-toolkit=3.0.47=pyha770c72_0
+  - psutil=6.0.0=py311h331c9d8_0
+  - pthread-stubs=0.3=h0ce48e5_1
+  - ptyprocess=0.7.0=pyhd3deb0d_0
+  - pure_eval=0.2.3=pyhd8ed1ab_0
+  - pybind11-abi=4=hd3eb1b0_1
+  - pycparser=2.21=pyhd3eb1b0_0
+  - python=3.11.9=h955ad1f_0
+  - python-dateutil=2.9.0post0=py311h06a4308_2
+  - python-tzdata=2023.3=pyhd3eb1b0_0
+  - python_abi=3.11=2_cp311
+  - pytz=2024.1=py311h06a4308_0
+  - pyzmq=25.1.2=py311h6a678d5_0
+  - r-assertthat=0.2.1=r43h6115d3f_0
+  - r-base=4.3.1=h1ae530e_0
+  - r-base64enc=0.1_3=r43h76d94ec_4
+  - r-biocmanager=1.30.22=r43h142f84f_0
+  - r-bitops=1.0_7=r43h76d94ec_0
+  - r-bslib=0.5.1=r43h6115d3f_0
+  - r-cachem=1.0.8=r43h76d94ec_0
+  - r-cairo=1.6_1=r43hec52ca5_0
+  - r-catools=1.18.2=r43h884c59f_0
+  - r-cli=3.6.1=r43h884c59f_0
+  - r-clue=0.3_65=r43h76d94ec_0
+  - r-cluster=2.1.4=r43h640688f_0
+  - r-codetools=0.2_19=r43h6115d3f_0
+  - r-colorspace=2.1_0=r43h76d94ec_0
+  - r-combinat=0.0_8=r43h142f84f_0
+  - r-cpp11=0.4.6=r43h6115d3f_0
+  - r-crayon=1.5.2=r43h6115d3f_0
+  - r-digest=0.6.33=r43h884c59f_0
+  - r-doparallel=1.0.17=r43h6115d3f_0
+  - r-dplyr=1.1.3=r43h884c59f_0
+  - r-ellipsis=0.3.2=r43h76d94ec_0
+  - r-evaluate=0.22=r43h6115d3f_0
+  - r-fansi=1.0.5=r43h76d94ec_0
+  - r-farver=2.1.1=r43h884c59f_0
+  - r-fastmap=1.1.1=r43h884c59f_0
+  - r-fmsb=0.7.5=r43h142f84f_0
+  - r-fontawesome=0.5.2=r43h6115d3f_0
+  - r-foreach=1.5.2=r43h6115d3f_0
+  - r-fs=1.6.3=r43h884c59f_0
+  - r-generics=0.1.3=r43h142f84f_0
+  - r-getoptlong=1.0.5=r43h6115d3f_0
+  - r-ggplot2=3.4.4=r43h6115d3f_0
+  - r-glmnet=4.1_8=r43hb5eb8f6_0
+  - r-globaloptions=0.1.2=r43h142f84f_0
+  - r-glue=1.6.2=r43h76d94ec_0
+  - r-gplots=3.1.3=r43h6115d3f_0
+  - r-gridbase=0.4_7=r43h6115d3f_4
+  - r-gridextra=2.3=r43h6115d3f_0
+  - r-gtable=0.3.4=r43h6115d3f_0
+  - r-gtools=3.9.4=r43h76d94ec_0
+  - r-highr=0.10=r43h6115d3f_0
+  - r-htmltools=0.5.6.1=r43h76d94ec_0
+  - r-infotheo=1.2.0.1=r43h884c59f_0
+  - r-isoband=0.2.7=r43h884c59f_0
+  - r-iterators=1.0.14=r43h6115d3f_0
+  - r-jquerylib=0.1.4=r43h6115d3f_0
+  - r-jsonlite=1.8.7=r43h76d94ec_0
+  - r-kernsmooth=2.23_22=r43h640688f_0
+  - r-knitr=1.44=r43h6115d3f_0
+  - r-labeling=0.4.3=r43h6115d3f_0
+  - r-lattice=0.22_5=r43h76d94ec_0
+  - r-lifecycle=1.0.3=r43h142f84f_0
+  - r-magrittr=2.0.3=r43h76d94ec_0
+  - r-mass=7.3_60=r43h76d94ec_0
+  - r-matrix=1.6_1.1=r43h76d94ec_0
+  - r-memoise=2.0.1=r43h6115d3f_0
+  - r-mgcv=1.9_0=r43h76d94ec_0
+  - r-mime=0.12=r43h76d94ec_0
+  - r-munsell=0.5.0=r43h6115d3f_0
+  - r-nlme=3.1_163=r43h640688f_0
+  - r-nmf=0.21.0=r43h884c59f_0
+  - r-nnls=1.5=r43h640688f_0
+  - r-pillar=1.9.0=r43h6115d3f_0
+  - r-pkgconfig=2.0.3=r43h6115d3f_0
+  - r-pkgmaker=0.32.10=r43h6115d3f_0
+  - r-plyr=1.8.9=r43h884c59f_0
+  - r-prettydoc=0.4.1=r43h142f84f_0
+  - r-purrr=1.0.2=r43h76d94ec_0
+  - r-r6=2.5.1=r43h6115d3f_0
+  - r-rappdirs=0.3.3=r43h76d94ec_0
+  - r-rcolorbrewer=1.1_3=r43h6115d3f_1
+  - r-rcpp=1.0.11=r43h884c59f_0
+  - r-rcppeigen=0.3.3.9.3=r43h884c59f_0
+  - r-registry=0.5_1=r43h6115d3f_0
+  - r-reshape2=1.4.4=r43h884c59f_0
+  - r-rjson=0.2.21=r43h884c59f_0
+  - r-rlang=1.1.1=r43h884c59f_0
+  - r-rmarkdown=2.25=r43h6115d3f_0
+  - r-rngtools=1.5.2=r43h6115d3f_0
+  - r-sass=0.4.7=r43h884c59f_0
+  - r-scales=1.2.1=r43h6115d3f_0
+  - r-shape=1.4.6=r43h142f84f_0
+  - r-stringi=1.7.12=r43h884c59f_0
+  - r-stringr=1.5.0=r43h6115d3f_0
+  - r-survival=3.5_7=r43h76d94ec_0
+  - r-tibble=3.2.1=r43h76d94ec_0
+  - r-tidyr=1.3.0=r43h884c59f_0
+  - r-tidyselect=1.2.0=r43h6115d3f_0
+  - r-tinytex=0.48=r43h142f84f_0
+  - r-utf8=1.2.4=r43h76d94ec_0
+  - r-vctrs=0.6.4=r43h884c59f_0
+  - r-viridis=0.6.4=r43h6115d3f_0
+  - r-viridislite=0.4.2=r43h6115d3f_0
+  - r-withr=2.5.1=r43h6115d3f_0
+  - r-xfun=0.40=r43h76d94ec_0
+  - r-xtable=1.8_4=r43h6115d3f_0
+  - r-yaml=2.3.7=r43h76d94ec_0
+  - readline=8.2=h5eee18b_0
+  - rpy2=3.5.11=py311r43h356210d_0
+  - scipy=1.13.1=py311h24aa872_0
+  - setuptools=69.5.1=py311h06a4308_0
+  - simplegeneric=0.8.1=py311h06a4308_2
+  - six=1.16.0=pyhd3eb1b0_1
+  - sqlite=3.45.3=h5eee18b_0
+  - stack_data=0.6.2=pyhd8ed1ab_0
+  - sysroot_linux-64=2.17=h57e8cba_10
+  - tk=8.6.14=h39e8969_0
+  - tktable=2.10=h3d55465_1
+  - tornado=6.4.1=py311h331c9d8_0
+  - traitlets=5.14.3=pyhd8ed1ab_0
+  - typing_extensions=4.12.2=pyha770c72_0
+  - tzdata=2024a=h04d1e81_0
+  - tzlocal=5.2=py311h06a4308_0
+  - wcwidth=0.2.13=pyhd8ed1ab_0
+  - wheel=0.43.0=py311h06a4308_0
+  - xorg-kbproto=1.0.7=h7f98852_1002
+  - xorg-libx11=1.8.9=hb711507_1
+  - xorg-libxau=1.0.11=hd590300_0
+  - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xorg-xextproto=7.3.0=h0b41bf4_1003
+  - xorg-xproto=7.0.31=h27cfd23_1007
+  - xz=5.4.6=h5eee18b_1
+  - zeromq=4.3.5=h6a678d5_0
+  - zipp=3.20.1=pyhd8ed1ab_0
+  - zlib=1.2.13=h5eee18b_1
+  - zstd=1.5.5=hc292b87_2
+  - pip:
+      - certifi==2024.8.30
+      - charset-normalizer==3.3.2
+      - colorama==0.4.6
+      - idna==3.8
+      - joblib==1.4.2
+      - kaleido==0.2.1
+      - metrics==0.3.3
+      - pathlib2==2.3.7.post1
+      - pathspec==0.5.5
+      - plotly==5.24.1
+      - pygments==2.2.0
+      - requests==2.32.3
+      - scikit-learn==1.5.1
+      - smgantt==0.0.5
+      - svm==0.1.0
+      - tenacity==9.0.0
+      - threadpoolctl==3.5.0
+      - urllib3==2.2.2
+      - xmltodict==0.13.0
+prefix: /home/nicolashomberg/miniconda3/envs/h3