Add spectra to docker #278
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1 error and 1 warning
Build Docker
buildx failed with: ERROR: failed to solve: process "/bin/sh -c apt-get update -y && apt-get upgrade -y && apt-get install -y libhdf5-dev python3-full python3-pip libpython3-dev inkscape librsvg2-bin locales locales-all wget git libxml2-dev libxslt-dev libgdal-dev libicu-dev libglpk-dev libbz2-dev \t cargo && rm -Rf /usr/lib/python3.12/EXTERNALLY-MANAGED && Rscript -e \"install.packages(c('remotes', 'devtools', 'BiocManager', 'pryr', 'rmdformats', 'knitr', 'logger', 'Matrix'), dependencies=TRUE, ask = FALSE, upgrade = 'always')\" && echo \"local({options(repos = BiocManager::repositories())})\" >> ~/.Rprofile && echo \"Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS='true');\" >> ~/.Rprofile && Rscript -e \"print(version)\" && apt-get remove --purge python3-numpy && python3 -m pip install \"numpy<2.0.0\" && python3 -m pip uninstall igraph && python3 -m pip install umap-learn phate scanpy sctour scSpectra scikit-misc celltypist scikit-learn leidenalg python-igraph && mkdir /conga && cd /conga && git clone https://github.com/phbradley/conga.git && cd conga/tcrdist_cpp && make && cd ../ && pip3 install -e . && cd / && export BC_BRANCH=`echo $R_BIOC_VERSION | sed 's/\\./_/'` && mkdir /bioconductor && cd /bioconductor && wget -O install_bioc_sysdeps.sh https://raw.githubusercontent.com/Bioconductor/bioconductor_docker/RELEASE_${BC_BRANCH}/bioc_scripts/install_bioc_sysdeps.sh && bash ./install_bioc_sysdeps.sh $R_BIOC_VERSION && cd / && rm -Rf /bioconductor && wget -O /bin/sda_static_linux https://www.dropbox.com/sh/chek4jkr28qnbrj/AADPy1qQlm3jsHPmPdNsjSx2a/bin/sda_static_linux?dl=1 && chmod +x /bin/sda_static_linux && pip3 install git+https://github.com/bbimber/demuxEM.git && pip3 install git+https://github.com/bbimber/GMM-Demux && apt-get clean && rm -rf /var/lib/apt/lists/* && pip3 cache purge \t&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds && mkdir /BiocFileCache && chmod 777 /BiocFileCache && mkdir /dockerHomeDir && chmod 777 /dockerHomeDir && mkdir /numba_cache && chmod -R 777 /numba_cache && mkdir /mpl_cache && chmod -R 777 /mpl_cache && mkdir /inkscape && chmod -R 777 /inkscape" did not complete successfully: exit code: 1
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Build Docker
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Artifacts
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bimberlabinternal~docker-base~HTWXDH.dockerbuild
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