Commit ba57aedf authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

picrust2 conda env extensions

parent 790dba35
......@@ -72,10 +72,11 @@ RUN pip3 install pysam numpy matplotlib checkm-genome && \
RUN python3 -m pip install gtdbtk
ENV GTDBTK_DATA_PATH=/unlock/references/databases/GTDBTK/release202/
## 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 env update --name picrust2 --file /picrust2_env.yml && \
conda deactivate
## Needed for faTools
......@@ -86,6 +87,7 @@ ENV CHECKM=/unlock/infrastructure/binaries/hmmer/hmmer-3.3.2/bin:/unlock/infrast
# note: CheckM and GTDB-Tk overlap with hmmer,prodigal and are not added to GTDBTK
ENV GTDBTK=/unlock/infrastructure/binaries/Mash/mash-Linux64-v2.3:/unlock/infrastructure/binaries/FastTree/FastTree_v2.1.11:/unlock/infrastructure/binaries/Mash/mash-Linux64-v2.3:/unlock/infrastructure/binaries/fastANI/fastANI_v1.33
ENV PATH=$PATH:$CHECKM:$GTDBTK
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