Commit 07d084e3 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

added HUMAnN meta-omics tools

parent 0ba677aa
......@@ -75,15 +75,23 @@ RUN pip3 install pysam numpy matplotlib checkm-genome && \
RUN python3 -m pip install gtdbtk
ENV GTDBTK_DATA_PATH=/unlock/references/databases/GTDBTK/release202/
## Needed for faTools (used in the metagenomics workflow)
RUN sudo ln -s /usr/lib/x86_64-linux-gnu/ /usr/lib/x86_64-linux-gnu/
## picrust2 (conda)
COPY conda/picrust2_env.yml /picrust2_env.yml
RUN source /root/miniconda/bin/activate && \
conda create -n picrust2 -c bioconda -c conda-forge picrust2=2.4.1 && \
conda update -n base -c defaults conda && \
conda create -v -n picrust2 -c bioconda -c conda-forge picrust2=2.4.1 && \
conda env update --name picrust2 --file /picrust2_env.yml && \
conda deactivate
## Needed for faTools
RUN sudo ln -s /usr/lib/x86_64-linux-gnu/ /usr/lib/x86_64-linux-gnu/
## HUMAnN meta-omics
RUN pip install humann --no-binary :all: && \
pip install metaphlan --no-binary :all: && \
humann_config --update database_folders nucleotide /unlock/references/databases/HUMAnN/chocophlan && \
humann_config --update database_folders utility_mapping /unlock/references/databases/HUMAnN/utility_mapping && \
humann_config --update database_folders protein /unlock/references/databases/HUMAnN/uniref
## SET PATH ##
ENV SDKMAN=/root/.sdkman/candidates/maven/current/bin:/root/.sdkman/candidates/java/current/bin:/root/.sdkman/candidates/gradle/current/bin
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