Commit 678428a1 authored by Jasper Koehorst's avatar Jasper Koehorst
Browse files

docker update

parent 0cad1841
......@@ -42,8 +42,9 @@ RUN chmod a+x "$HOME/.sdkman/bin/sdkman-init.sh"
RUN echo "sdkman_auto_complete=false" >> "$HOME/.sdkman/etc/config"
RUN source "$HOME/.sdkman/bin/sdkman-init.sh" &&\
sdk install java 11.0.11.hs-adpt &&\
sdk install gradle 7.1 &&\
sdk install maven 3.6.3
sdk install gradle 7.1 && \
sdk install maven 3.6.3 && \
rm -r /root/.sdkman/archives
# R
RUN apt-get update && apt-get install -y software-properties-common && \
......@@ -54,7 +55,8 @@ RUN apt-get update && apt-get install -y software-properties-common && \
# Miniconda
RUN wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
bash /Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda
bash /Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda && \
rm Miniconda3-latest-Linux-x86_64.sh
######################################
####### ANALYSIS TOOLS SECTION #######
......@@ -82,7 +84,8 @@ RUN source /root/miniconda/bin/activate && \
pip install --editable . && \
conda env update --name picrust2 --file /picrust2_env.yml && \
conda deactivate && \
rm /picrust2_env.yml
# conda clean && \
rm /picrust2_env.yml /v2.4.1.tar.gz
## HUMAnN meta-omics
RUN python3 -m pip install humann --no-binary :all: && \
......
......@@ -61,10 +61,17 @@ grep "[0-9]\+_irods:" $yaml | awk '{print $2}' | sort | uniq | awk '{print "java
# Start a conda environment when needed
conda_env=`grep conda $yaml | awk -F": " '{print $2}'`
echo "CONDA ENV = $conda_env"
if ! [[ -z "$conda_env" ]]; then
echo "Starting conda environment in $conda_env"
source /root/miniconda/bin/activate && conda activate $conda_env
# Test to see if rdflib is available
python3 -c "import rdflib"
exit_status=$?
if [ $exit_status -ne 0 ]; then
echo "RDFLib not available $exit_status"
exit
fi
fi
# Run workflow with or without provenance
......
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