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