🚧 specify packages in command, use chmod on tb-profiler/share/

Author: victorlin

Dockerfile

@@ -14,16 +14,24 @@ ENV PATH="/nextstrain/miniforge/bin:$PATH"
 # Initialize conda for interactive shell use
 RUN conda init bash
 
-# FIXME: is `umask 000` ok to use here?
-# This allows commands like `tb-profiler update_tbdb` to write to
-# /nextstrain/miniforge/envs/tb-profiler/share/tbprofiler/
 
 # Create conda environments
-COPY --chown=nextstrain:nextstrain envs/snippy.yaml /tmp/
-RUN umask 000 && conda env create --name snippy --file /tmp/snippy.yaml && rm /tmp/snippy.yaml
 
-COPY --chown=nextstrain:nextstrain envs/tb-profiler.yaml /tmp/
-RUN umask 000 && conda env create --name tb-profiler --file /tmp/tb-profiler.yaml && rm /tmp/tb-profiler.yaml
+RUN conda create -y --name snippy \
+      -c conda-forge -c bioconda \
+      sra-tools=3.2.1 \
+      snippy=4.6.0 \
+ && conda clean -afy \
+
+# chmod allows `tb-profiler update_tbdb` to write to
+# /nextstrain/miniforge/envs/tb-profiler/share/tbprofiler/
+RUN conda create -y --name tb-profiler \
+      -c conda-forge -c bioconda \
+      sra-tools=3.2.1 \
+      tb-profiler=6.6.3-0 \
+ && conda clean -afy \
+ && chmod -R u+w /nextstrain/miniforge/envs/tb-profiler/share/
+
 
 # Switch back to root.  The entrypoint will drop to nextstrain:nextstrain as
 # necessary when a container starts.