Mercurial > repos > jpayne > seqsero2s

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planemo upload commit 6caed405f48e5af3f645120593a6df3efdb7f2a0
author galaxytrakr
date Fri, 25 Sep 2026 20:13:08 +0000
parents c449145d54cb
children
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23:c449145d54cb 24:3825e0f45380
48 spades>=3.9 \ 48 spades>=3.9 \
49 salmid \ 49 salmid \
50 bwa>=0.7 \ 50 bwa>=0.7 \
51 seqtk>=1.3 \ 51 seqtk>=1.3 \
52 stringmlst>=0.6 \ 52 stringmlst>=0.6 \
53 perl-list-moreutils \
54 && mamba create -n mlst_env -c conda-forge -c bioconda \
53 mlst>=2.32 \ 55 mlst>=2.32 \
54 perl-list-moreutils \
55 && mamba clean -afy 56 && mamba clean -afy
57
58
56 59
57 # Install SeqSero2S from local fork 60 # Install SeqSero2S from local fork
58 WORKDIR /tmp/build/SeqSero2S 61 WORKDIR /tmp/build/SeqSero2S
59 62
60 # Copy the current build context (the cloned source code) into the container. 63 # Copy the current build context (the cloned source code) into the container.
86 echo "SeqSero2S.py -h: PASSED" && \ 89 echo "SeqSero2S.py -h: PASSED" && \
87 /opt/conda/envs/seqsero2s/bin/blastn -help && \ 90 /opt/conda/envs/seqsero2s/bin/blastn -help && \
88 echo "blastn -help: PASSED" && \ 91 echo "blastn -help: PASSED" && \
89 /opt/conda/envs/seqsero2s/bin/SalmID.py -h && \ 92 /opt/conda/envs/seqsero2s/bin/SalmID.py -h && \
90 echo "SalmID.py -h: PASSED" && \ 93 echo "SalmID.py -h: PASSED" && \
91 /opt/conda/envs/seqsero2s/bin/mlst -h && \ 94 /opt/conda/envs/mlst_env/bin/mlst -h && \
92 echo "mlst -h: PASSED" && \ 95 echo "mlst -h: PASSED" && \
93 echo "All tests completed successfully!" 96 echo "All tests completed successfully!"
94 97
95 # Default command shows test results 98 # Default command shows test results
96 CMD ["echo", "All SeqSero2S tests passed successfully!"] 99 CMD ["echo", "All SeqSero2S tests passed successfully!"]
100 # ============================================================================ 103 # ============================================================================
101 FROM condaforge/mambaforge:latest AS dist 104 FROM condaforge/mambaforge:latest AS dist
102 105
103 # Copy conda environment from builder 106 # Copy conda environment from builder
104 COPY --from=builder /opt/conda/envs/seqsero2s /opt/conda/envs/seqsero2s 107 COPY --from=builder /opt/conda/envs/seqsero2s /opt/conda/envs/seqsero2s
108 COPY --from=builder /opt/conda/envs/mlst_env /opt/conda/envs/mlst_env
105 109
106 # Update PATH to use the conda environment 110 # Update PATH to use the conda environment
107 ENV PATH=/opt/conda/envs/seqsero2s/bin:$PATH \ 111 ENV PATH=/opt/conda/envs/mlst_env/bin:/opt/conda/envs/seqsero2s/bin:$PATH \
108 CONDA_DEFAULT_ENV=seqsero2s \ 112 CONDA_DEFAULT_ENV=seqsero2s \
109 CONDA_PREFIX=/opt/conda/envs/seqsero2s 113 CONDA_PREFIX=/opt/conda/envs/seqsero2s
110 114
111 # Install minimal runtime dependencies 115 # Install minimal runtime dependencies
112 RUN apt-get update && \ 116 RUN apt-get update && \