Merge pull request #44 from broadinstitute/ct-bump-viral-core-2.3.1

update viral-core 2.2.4 -> 2.3.1 (w/ python 3.8 -> 3.10)

Dockerfile

@@ -1,20 +1,32 @@
-FROM quay.io/broadinstitute/viral-core:2.2.4
+FROM quay.io/broadinstitute/viral-core:2.3.1
 
 LABEL maintainer "viral-ngs@broadinstitute.org"
 
 ENV VIRAL_CLASSIFY_PATH=$INSTALL_PATH/viral-classify \
-	PATH="$PATH:$MINICONDA_PATH/envs/env2/bin"
+	PATH="$PATH:$MINICONDA_PATH/envs/env2/bin:$MINICONDA_PATH/envs/env3/bin:$MINICONDA_PATH/envs/env4/bin"
 
-COPY requirements-conda.txt requirements-conda-env2.txt $VIRAL_CLASSIFY_PATH/
+COPY requirements-conda.txt requirements-conda-env2.txt requirements-conda-env3.txt requirements-conda-env4.txt $VIRAL_CLASSIFY_PATH/
 # install most dependencies to the main environment
 RUN $VIRAL_NGS_PATH/docker/install-conda-dependencies.sh $VIRAL_CLASSIFY_PATH/requirements-conda.txt $VIRAL_NGS_PATH/requirements-conda.txt
 
 # install packages with dependency incompatibilities to the second environment
 RUN CONDA_PREFIX="$MINICONDA_PATH/envs/env2"; \
-	conda config --set channel_priority strict; \
+	#conda config --set channel_priority strict; \
 	conda create -q -y -n env2; \
 	$VIRAL_NGS_PATH/docker/install-conda-dependencies.sh $VIRAL_CLASSIFY_PATH/requirements-conda-env2.txt
 
+# install packages with dependency incompatibilities to the third environment
+RUN CONDA_PREFIX="$MINICONDA_PATH/envs/env3"; \
+	#conda config --set channel_priority strict; \
+	conda create -q -y -n env3; \
+	$VIRAL_NGS_PATH/docker/install-conda-dependencies.sh $VIRAL_CLASSIFY_PATH/requirements-conda-env3.txt
+
+# install packages with dependency incompatibilities to the 4th environment
+RUN CONDA_PREFIX="$MINICONDA_PATH/envs/env4"; \
+	#conda config --set channel_priority strict; \
+	conda create -q -y -n env4; \
+	$VIRAL_NGS_PATH/docker/install-conda-dependencies.sh $VIRAL_CLASSIFY_PATH/requirements-conda-env4.txt
+
 # Copy all source code into the base repo
 # (this probably changes all the time, so all downstream build
 # layers will likely need to be rebuilt each time)

docs/requirements.txt

@@ -2,7 +2,7 @@ jinja2==3.1.2 # https://github.com/readthedocs/readthedocs.org/issues/9037#issue
 Sphinx==5.3.0 #override sphinx pinning done by RTD: https://docs.readthedocs.io/en/stable/build-default-versions.html#external-dependencies
 sphinx-argparse
 sphinx-rtd-theme==1.1.1
-matplotlib==2.2.4
+matplotlib>=2.2.4
 PyYAML==6.0
 mock==5.0.1
 recommonmark

requirements-conda-env3.txt

@@ -0,0 +1 @@
+diamond>=2.1.9

requirements-conda-env4.txt

@@ -0,0 +1,2 @@
+kraken2>=2.1.3
+krona>=2.8.1

requirements-conda.txt

@@ -1,7 +1,5 @@
-blast>=2.9.0
+blast>=2.15.0
 bmtagger>=3.101
-diamond>=2.1.9
 kmc>=3.2.1
-kraken2>=2.1.3
-krona>=2.8.1
 last>=1541
+perl>=5.22.0,<5.23.0