Commit 40cbb362 authored by josh's avatar josh
Browse files

switch to python3 versions of packages

many python2 versions of packages are no longer in ubuntu 20.04
parent 59bdc9e2
Pipeline #193118 passed with stages
in 179 minutes and 27 seconds
......@@ -170,7 +170,7 @@ RUN apt-get update && \
software-properties-common \
libgdal-dev \
build-essential \
python-dev \
python3-dev \
python3-pip \
python3-numpy \
python3-matplotlib \
......@@ -256,17 +256,11 @@ RUN Rscript -e "install.packages(pkgs = c('coin'), \
# python libraries: rpy2 (v. 2.1 or higher), numpy, matplotlib (v. 1.0 or higher), argparse
RUN apt-get update && \
apt-get -yq install \
python-rpy2
RUN apt-get update && \
apt-get install -y --no-install-recommends \
python-h5py
RUN apt-get update && \
apt-get install -y --no-install-recommends \
nano \
jed
apt-get install -y --no-install-recommends \
python3-rpy2 \
python3-h5py \
nano \
jed
RUN mkdir -p $MANUAL_BIN && \
cd $MANUAL_BIN && \
......@@ -280,11 +274,6 @@ RUN mkdir -p $MANUAL_BIN && \
# USER $RSTUDIO_USER
RUN apt-get update && \
apt-get install -yq --no-install-recommends \
python-h5py
##------------------------------------------------------------
# install fastq-mcf and fastq-multx from source since apt-get install causes problems
RUN mkdir -p /usr/bin && \
......@@ -382,6 +371,7 @@ RUN mkdir kaiju && \
tar -zx -C kaiju --strip-components=1 && \
cd kaiju/src && \
make && \
cd ../.. && \
mv kaiju/bin/* $MANUAL_BIN && \
rm -rf kaiju
......
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