From 5f82d0a7021b39fe81f6ec62d965e2712fcfdc4c Mon Sep 17 00:00:00 2001 From: Candice Date: Mon, 1 Jun 2020 16:13:30 +0200 Subject: [PATCH] luslab-umitools | Customized Dockerfile for umi_tools --- tools/umi_tools/Dockerfile | 22 ++-------------------- 1 file changed, 2 insertions(+), 20 deletions(-) diff --git a/tools/umi_tools/Dockerfile b/tools/umi_tools/Dockerfile index f7a9099f..636c051a 100644 --- a/tools/umi_tools/Dockerfile +++ b/tools/umi_tools/Dockerfile @@ -1,6 +1,6 @@ FROM continuumio/miniconda3:4.8.2 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 RUN apt-get update \ @@ -17,25 +17,7 @@ RUN apt-get update \ # Install conda packages COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a -ENV PATH /opt/conda/envs/luslab-clip-0.1/bin:$PATH - -# Install Paraclu -WORKDIR /home -RUN mkdir bin && wget http://cbrc3.cbrc.jp/~martin/paraclu/paraclu-9.zip && unzip paraclu-9.zip -WORKDIR /home/paraclu-9 -RUN make && cp paraclu /home/bin/paraclu && cp paraclu-cut.sh /home/bin/paraclu-cut.sh - -# Install PEKA -WORKDIR /home -RUN wget https://raw.githubusercontent.com/ulelab/imaps/master/src/imaps/sandbox/kmers.py -RUN mkdir src && mv kmers.py src/kmers.py - -# Install iCount -WORKDIR /home -RUN wget https://github.com/tomazc/iCount/archive/master.zip && mv master.zip icount.zip && unzip icount.zip -WORKDIR /home/iCount-master -# hadolint ignore=SC2102,DL3013 -RUN pip install -e .[test] +ENV PATH /opt/conda/envs/nfcore-umitools-0.1/bin:$PATH # Reset work dir WORKDIR /home \ No newline at end of file