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Commit message:
planemo upload commit 34fc6bf8421ce1ff1f9dc7cfbb2317430569acdc |
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modified:
Dockerfile |
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| diff -r b15b07ad729b -r 790b6c0e71fb Dockerfile --- a/Dockerfile Fri May 15 14:05:53 2026 +0000 +++ b/Dockerfile Fri May 15 16:59:42 2026 +0000 |
| [ |
| @@ -27,16 +27,12 @@ # Update base packages and install build essentials RUN apt-get update && \ apt-get install -y --no-install-recommends \ - wget \ - ca-certificates \ - bash \ + wget \ + ca-certificates \ + bash \ && apt-get clean && \ rm -rf /var/lib/apt/lists/* -# Copy the patch script -COPY patch_stringmlst.sh /tmp/patch_stringmlst.sh -RUN chmod +x /tmp/patch_stringmlst.sh - # Create conda environment with all dependencies # Using mamba for faster dependency resolution RUN mamba create -n seqsero2s -c conda-forge -c bioconda \ @@ -58,18 +54,22 @@ && mamba clean -afy # Install SeqSero2S from local fork -WORKDIR /tmp/build +WORKDIR /tmp/build/SeqSero2S -# Copy local SeqSero2S directory -COPY SeqSero2S /tmp/build/SeqSero2S +# Copy the current build context (the cloned source code) into the container. +COPY . . # Install SeqSero2S -RUN cd SeqSero2S && \ - /opt/conda/envs/seqsero2s/bin/python -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir +RUN /opt/conda/envs/seqsero2s/bin/python -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir -# Apply the stringMLST.py patch (from the conda recipe) -# The patch replaces dbPrefix reference with cwd to avoid path issues -RUN PREFIX=/opt/conda/envs/seqsero2s /tmp/patch_stringmlst.sh +# Apply the stringMLST.py patch inline using 'sed'. +# This exactly replicates the original python patch script by commenting out the old line and adding the new one. +RUN if [ -f "/opt/conda/envs/seqsero2s/bin/stringMLST.py" ]; then \ + sed -i 's| log = dbPrefix+'\''.log'\''| # log = dbPrefix+'\''.log'\''\n log = os.path.join(os.getcwd(), "kmer.log")|g' /opt/conda/envs/seqsero2s/bin/stringMLST.py && \ + echo "PATCHED: stringMLST.py log path fixed"; \ + else \ + echo "SKIP: stringMLST.py not found"; \ + fi # ============================================================================ # Stage 3: Test image - runs validation tests @@ -110,8 +110,8 @@ # Install minimal runtime dependencies RUN apt-get update && \ apt-get install -y --no-install-recommends \ - ca-certificates \ - procps \ + ca-certificates \ + procps \ && apt-get clean && \ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* @@ -121,7 +121,6 @@ # Create non-root user for running the application RUN useradd -m -u 1000 -s /bin/bash seqsero2s && \ chown -R seqsero2s:seqsero2s /data - USER seqsero2s # Add metadata labels @@ -135,3 +134,5 @@ org.opencontainers.image.description="Simplified Salmonella serotype prediction from genome sequencing data" # No entrypoint or command for dist target + + |