# HG changeset patch
# User galaxytrakr
# Date 1790367188 0
# Node ID 3825e0f4538084f38f2e3547cde77f059e0a8dde
# Parent  c449145d54cbd6fce09d1503e84e0e22501db18f
planemo upload commit 6caed405f48e5af3f645120593a6df3efdb7f2a0

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
@@ -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