From f598198e7b8c9350c08f223750708e905ef4ce99 Mon Sep 17 00:00:00 2001 From: Sam Date: Mon, 18 Mar 2024 10:18:38 -0600 Subject: [PATCH] restore slash, replace fastp with trimmomatic and flash, add autoremove step --- Dockerfile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index c3dc4060..699d26d1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,10 +10,11 @@ MAINTAINER Kendell Clement RUN apt-get update && apt-get install gcc g++ bowtie2 samtools libsys-hostname-long-perl \ -y --no-install-recommends \ && apt-get clean \ + && apt-get autoremove -y \ && rm -rf /var/lib/apt/lists/* \ && rm -rf /usr/share/man/* \ && rm -rf /usr/share/doc/* \ - && conda install -c defaults -c conda-forge -c bioconda -y -n base --debug fastp numpy cython jinja2 tbb=2020.2 pyparsing=2.3.1 scipy matplotlib-base pandas plotly\ + && conda install -c defaults -c conda-forge -c bioconda -y -n base --debug trimmomatic flash numpy cython jinja2 tbb=2020.2 pyparsing=2.3.1 scipy matplotlib-base pandas plotly\ && conda clean --all --yes #install ms fonts @@ -32,7 +33,7 @@ RUN echo "deb http://httpredir.debian.org/debian buster main contrib" > /etc/apt # install crispresso COPY . /CRISPResso2 WORKDIR /CRISPResso2 -RUN python setup.py install +RUN python setup.py install \ && CRISPResso -h \ && CRISPRessoBatch -h \ && CRISPRessoPooled -h \