Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix: use mambaforge for snakemake container image #1595

Merged
merged 2 commits into from Apr 22, 2022
Merged

fix: use mambaforge for snakemake container image #1595

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
284a4a0
fix: use mambaforge for snakemake container image
johanneskoester Apr 22, 2022
c604dc0
Merge branch 'main' into mambaforge
johanneskoester Apr 22, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
9 changes: 4 additions & 5 deletions Dockerfile
View file
Open in desktop
Expand Up @@ -6,11 +6,10 @@ ENV PATH /opt/conda/bin:${PATH}
ENV LANG C.UTF-8
ENV SHELL /bin/bash
RUN install_packages wget curl bzip2 ca-certificates gnupg2 squashfs-tools git
RUN /bin/bash -c "curl -L https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh > miniconda.sh && \
bash miniconda.sh -b -p /opt/conda && \
rm miniconda.sh"
RUN /bin/bash -c "conda install -y -c conda-forge mamba && \
mamba create -q -y -c conda-forge -c bioconda -n snakemake snakemake snakemake-minimal --only-deps && \
RUN /bin/bash -c "curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh > mambaforge.sh && \
bash mambaforge.sh -b -p /opt/conda && \
rm mambaforge.sh"
RUN /bin/bash -c "mamba create -q -y -c conda-forge -c bioconda -n snakemake snakemake snakemake-minimal --only-deps && \
source activate snakemake && \
mamba install -q -y -c conda-forge singularity && \
conda clean --all -y && \
Expand Down