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luslab-umitools | Customized Dockerfile for umi_tools

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Candice 2020-06-01 16:13:30 +02:00
parent 7cc1319801
commit 5f82d0a702
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tools/umi_tools/Dockerfile
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@ -1,6 +1,6 @@
FROM continuumio/miniconda3:4.8.2 FROM continuumio/miniconda3:4.8.2
LABEL authors="chris.cheshire@crick.ac.uk" \ LABEL authors="chris.cheshire@crick.ac.uk" \
description="Docker image containing all requirements for the luslab/group-nextflow-clip pipeline" description="Docker image containing all requirements for the nf-core umi_tools module"
# Install apt packages # Install apt packages
RUN apt-get update \ RUN apt-get update \
@ -17,25 +17,7 @@ RUN apt-get update \
# Install conda packages # Install conda packages
COPY environment.yml / COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/luslab-clip-0.1/bin:$PATH ENV PATH /opt/conda/envs/nfcore-umitools-0.1/bin:$PATH
# Install Paraclu
WORKDIR /home
RUN mkdir bin && wget http://cbrc3.cbrc.jp/~martin/paraclu/paraclu-9.zip && unzip paraclu-9.zip
WORKDIR /home/paraclu-9
RUN make && cp paraclu /home/bin/paraclu && cp paraclu-cut.sh /home/bin/paraclu-cut.sh
# Install PEKA
WORKDIR /home
RUN wget https://raw.githubusercontent.com/ulelab/imaps/master/src/imaps/sandbox/kmers.py
RUN mkdir src && mv kmers.py src/kmers.py
# Install iCount
WORKDIR /home
RUN wget https://github.com/tomazc/iCount/archive/master.zip && mv master.zip icount.zip && unzip icount.zip
WORKDIR /home/iCount-master
# hadolint ignore=SC2102,DL3013
RUN pip install -e .[test]
# Reset work dir # Reset work dir
WORKDIR /home WORKDIR /home