| Previous changeset 23:c449145d54cb (2026-09-25) |
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Commit message:
planemo upload commit 6caed405f48e5af3f645120593a6df3efdb7f2a0 |
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modified:
Dockerfile |
| b |
| diff -r c449145d54cb -r 3825e0f45380 Dockerfile --- a/Dockerfile Fri Sep 25 16:57:57 2026 +0000 +++ b/Dockerfile Fri Sep 25 20:13:08 2026 +0000 |
| b |
| @@ -50,10 +50,13 @@ bwa>=0.7 \ seqtk>=1.3 \ stringmlst>=0.6 \ + perl-list-moreutils \ + && mamba create -n mlst_env -c conda-forge -c bioconda \ mlst>=2.32 \ - perl-list-moreutils \ && mamba clean -afy + + # Install SeqSero2S from local fork WORKDIR /tmp/build/SeqSero2S @@ -88,7 +91,7 @@ echo "blastn -help: PASSED" && \ /opt/conda/envs/seqsero2s/bin/SalmID.py -h && \ echo "SalmID.py -h: PASSED" && \ - /opt/conda/envs/seqsero2s/bin/mlst -h && \ + /opt/conda/envs/mlst_env/bin/mlst -h && \ echo "mlst -h: PASSED" && \ echo "All tests completed successfully!" @@ -102,9 +105,10 @@ # Copy conda environment from builder COPY --from=builder /opt/conda/envs/seqsero2s /opt/conda/envs/seqsero2s +COPY --from=builder /opt/conda/envs/mlst_env /opt/conda/envs/mlst_env # Update PATH to use the conda environment -ENV PATH=/opt/conda/envs/seqsero2s/bin:$PATH \ +ENV PATH=/opt/conda/envs/mlst_env/bin:/opt/conda/envs/seqsero2s/bin:$PATH \ CONDA_DEFAULT_ENV=seqsero2s \ CONDA_PREFIX=/opt/conda/envs/seqsero2s |