Commit 830a04a9 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

CheckM tool added

parent 5ee54f1d
......@@ -64,7 +64,7 @@ LABEL tags="Base"
ENV DEBIAN_FRONTEND=noninteractive LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LANGUAGE=en_US.UTF-8
# Install the CWL runner (cwltool)
# Install the CWL runner (cwltool) and pip
RUN apt-get update && apt-get install -y wget curl pigz nodejs build-essential cpanminus git python3 python3-dev python3-distutils && \
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && python3 get-pip.py && \
pip3 install cwltool &&\
......@@ -102,13 +102,17 @@ RUN apt install -y software-properties-common && \
apt install -y r-base
# FastqPuri (RNAseq pre-processing) dependencies
RUN R -e "install.packages(c('pheatmap', 'knitr', 'rmarkdown' ,'stringr'))"
# RUN R -e "install.packages(c('pheatmap', 'knitr', 'rmarkdown' ,'stringr'))"
# Quast
RUN pip install quast
# Fix locale issue with quast
RUN apt-get clean && apt-get update && apt-get install -y locales nano htop libfontconfig1 && locale-gen en_US.UTF-8 && dpkg-reconfigure locales
# CheckM
ENV PATH=$PATH:/unlock/infrastructure/binaries/hmmer/hmmer-3.3.2/bin/:/unlock/infrastructure/binaries/pplacer/pplacer-Linux-v1.1.alpha17/bin/:/unlock/infrastructure/binaries/prodigal/v2.6.3/
RUN pip3 install pysam numpy matplotlib checkm-genome && \
checkm data setRoot /unlock/references/databases/CheckM/
# Add anonymous access
ADD irods /root/.irods
......
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