diff --git a/Dockerfile b/Dockerfile index 6b1af2b..085d570 100644 --- a/Dockerfile +++ b/Dockerfile @@ -28,7 +28,7 @@ COPY --chown=$MAMBA_USER:$MAMBA_USER env_a.yaml /tmp/env_a.yaml COPY --chown=$MAMBA_USER:$MAMBA_USER env_b.yaml /tmp/env_b.yaml COPY --chown=$MAMBA_USER:$MAMBA_USER env_f.yaml /tmp/env_f.yaml -RUN micromamba install -y -n base -f /tmp/env.yaml && \ +RUN micromamba create -y -f /tmp/env.yaml && \ micromamba create -y -f /tmp/env_a.yaml && \ micromamba create -y -f /tmp/env_b.yaml && \ micromamba create -y -f /tmp/env_f.yaml && \ @@ -37,10 +37,7 @@ RUN micromamba install -y -n base -f /tmp/env.yaml && \ FROM mambaorg/micromamba:2.0.2 COPY --from=JAFFA /JAFFA /JAFFA COPY --from=Fusim /opt/ /bin/ -COPY --from=envbuilder /opt/conda/bin/ /opt/base/ -COPY --from=envbuilder /opt/conda/envs/arriba/bin/ /opt/arriba/ -COPY --from=envbuilder /opt/conda/envs/fusionseeker/bin/ /opt/fusionseeker/ -COPY --from=envbuilder /opt/conda/envs/starfusion/bin/ /opt/starfusion/ +COPY --from=envbuilder /opt/conda/envs/ /opt/conda/envs/ ENV DEBIAN_FRONTEND=noninteractive @@ -53,7 +50,7 @@ RUN R -q -e "install.packages(c('curl'))" && \ Rscript -e "install.packages('BiocManager', dependencies=TRUE, repos='http://cran.rstudio.com/')" && \ Rscript -e "BiocManager::install(c('GenomicFeatures', 'Biostrings', 'biomaRt', 'rtracklayer', 'stringr', 'ggplot2', 'patchwork', 'cowplot'))" -ENV PATH="/opt/arriba:/opt/starfusion:/opt/fusionseeker:/opt/base:/bin:/JAFFA/tools/bin:/JAFFA:/bin/fusim-0.2.2:/bin/Fusionseeker:$PATH" +ENV PATH="/opt/conda/envs/arriba:/opt/conda/envs/fusionseeker:/opt/conda/envs/starfusion:/opt/conda/envs/normal:/bin:/JAFFA/tools/bin:/JAFFA:/bin/fusim-0.2.2:/bin/Fusionseeker:$PATH" COPY ./src /src COPY ./models /model diff --git a/env.yaml b/env.yaml index 2156eb2..8688d66 100644 --- a/env.yaml +++ b/env.yaml @@ -1,4 +1,4 @@ -name: base +name: normal channels: - conda-forge - bioconda