Create conda environments at build time

Author: victorlin

Dockerfile

@@ -9,3 +9,19 @@ RUN curl -L "https://github.com/conda-forge/miniforge/releases/latest/download/M
 
 # Make conda available in PATH
 ENV PATH="/nextstrain/miniforge/bin:$PATH"
+
+# Create conda environments
+COPY envs/csvtk.yaml /tmp/
+RUN conda env create --name csvtk --file /tmp/csvtk.yaml && rm /tmp/csvtk.yaml
+
+COPY envs/nextstrain.yaml /tmp/
+RUN conda env create --name nextstrain --file /tmp/nextstrain.yaml && rm /tmp/nextstrain.yaml
+
+COPY envs/snippy.yaml /tmp/
+RUN conda env create --name snippy --file /tmp/snippy.yaml && rm /tmp/snippy.yaml
+
+COPY envs/tb-profiler.yaml /tmp/
+RUN conda env create --name tb-profiler --file /tmp/tb-profiler.yaml && rm /tmp/tb-profiler.yaml
+
+COPY envs/tsv-utils.yaml /tmp/
+RUN conda env create --name tsv-utils --file /tmp/tsv-utils.yaml && rm /tmp/tsv-utils.yaml

envs/csvtk.yaml

@@ -0,0 +1,4 @@
+channels:
+  - conda-forge
+dependencies:
+  - csvtk

env.yaml envs/nextstrain.yamlenv.yaml renamed to envs/nextstrain.yaml

@@ -1,8 +1,5 @@
-name: env
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
 dependencies:
-  - sra-tools
-  - snippy
-  - tb-profiler=6
+  - augur=27.1.0

envs/snippy.yaml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - sra-tools=3.2.1
+  - snippy=4.6.0=hdfd78af_6
+  - awscli

envs/tb-profiler.yaml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - sra-tools=3.2.1
+  - tb-profiler=6.6.3-0
+  - awscli

envs/tsv-utils.yaml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - tsv-utils