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# Copyright (c) Bioinformatics Core Facility of the Max Planck Institute for Biology of Ageing.
# Distributed under the terms of the Modified BSD License.
# Debian buster-slim (10.1) image available on 20 Wednesday 2020.
FROM debian@sha256:11253793361a12861562d1d7b15b8b7e25ac30dd631e3d206ed1ca969bf97b7d
LABEL maintainer "bioinformatics@age.mpg.de"
USER root
ENV DEBIAN_FRONTEND noninteractive
ENV MODS /modules
ENV SOFT $MODS/software
ENV SOUR $MODS/sources/
ENV MODF $MODS/modulefiles
ENV LOGS $MODS/installation_logs
RUN mkdir -p $SOFT $SOUR $MODF $LOGS $MODF/bioinformatics $MODF/general $MODF/libs
RUN echo "deb http://ftp.debian.org/debian buster main non-free contrib" >> /etc/apt/sources.list && \
echo "deb-src http://ftp.debian.org/debian buster main non-free contrib" >> /etc/apt/sources.list && \
echo "deb http://ftp.debian.org/debian buster-updates main contrib non-free" >> /etc/apt/sources.list && \
echo "deb-src http://ftp.debian.org/debian buster-updates main contrib non-free" >> /etc/apt/sources.list
RUN REPO=http://cdn-fastly.deb.debian.org && \
echo "deb $REPO/debian buster main\ndeb $REPO/debian-security buster/updates main" > /etc/apt/sources.list && \
apt-get update && apt-get -yq dist-upgrade && \
apt-get install -yq --no-install-recommends locales && \
apt-get clean && rm -rf /var/lib/apt/lists/* && \
echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && locale-gen
RUN apt-get update && \
apt-get install -yq --no-install-recommends \
libreadline-dev \
xorg-dev \
apt-utils \
wget \
bzip2 \
ca-certificates \
sudo \
jed \
emacs \
build-essential \
python-dev \
unzip \
libsm6 \
pkg-config \
pigz \
zlib1g-dev \
autoconf \
automake \
environment-modules \
gcc && \
apt-get clean && rm -rf /var/lib/apt/lists/*
RUN apt-get update && \
apt-get install -yq --no-install-recommends \
f2c \
git \
vim \
texlive-latex-base \
texlive-latex-extra \
texlive-fonts-extra \
texlive-fonts-recommended \
pandoc \
texlive-generic-recommended \
libxrender1 \
inkscape \
libxml2-dev \
libcurl4-gnutls-dev \
libatlas3-base \
libopenblas-base \
libfreetype6-dev \
libtool \
libexpat1-dev \
libxml2-dev \
libxslt1-dev && \
apt-get clean && rm -rf /var/lib/apt/lists/*
RUN apt-get update && \
apt-get install -yq --no-install-recommends \
ghostscript \
gfortran \
libpcre3 \
libpcre3-dev \
libssl-dev \
libsqlite3-dev \
libssl-dev \
libfreetype6-dev \
libpng-dev \
liblmdb-dev \
libmariadb-dev \
libmariadb-client-lgpl-dev-compat \
libtbb2 \
libtbb-dev \
curl \
libcurl4 \
libcurl4-openssl-dev \
libncurses5-dev \
libcairo2-dev \
libtool-bin \
libzmq3-dev \
zip && \
apt-get clean && rm -rf /var/lib/apt/lists/*
RUN apt-get update && \
apt-get install -yq --no-install-recommends \
tk \
tcl \
openssl \
libssl-dev \
libssh2-1-dev \
libtool \
libffi-dev \
ruby \
ruby-dev \
make \
libzmq3-dev \
libczmq-dev \
apt-transport-https \
dirmngr \
cmake \
libpam0g-dev \
lsb-release \
libedit2 \
libapparmor1 \
gnupg \
liblzma-dev \
psmisc \
less \
libclang-dev && \
apt-get clean && rm -rf /var/lib/apt/lists/*
RUN cd ${SOUR} && \
wget http://ftp.de.debian.org/debian/pool/main/o/openssl/libssl1.1_1.1.1d-0+deb10u2_amd64.deb && \
dpkg -i libssl1.1_1.1.1d-0+deb10u2_amd64.deb && \
rm -rf ${SOUR}/*
RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 3FA7E0328081BFF6A14DA29AA6A19B38D3D831EF && \
echo "deb https://download.mono-project.com/repo/debian stable-buster main" | sudo tee /etc/apt/sources.list.d/mono-official-stable.list && \
apt update && apt-get -y install mono-devel && apt-get clean && rm -rf /var/lib/apt/lists/*
ENV SHELL /bin/bash
ENV NB_USER mpiage
ENV NB_UID 1000
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US.UTF-8
RUN useradd -m -s /bin/bash -N -u $NB_UID $NB_USER ; \
echo "root:bioinf" | chpasswd ; \
echo "mpiage:bioinf" | chpasswd ; \
adduser mpiage sudo
# Install Tini
RUN wget --quiet https://github.com/krallin/tini/releases/download/v0.10.0/tini && \
echo "1361527f39190a7338a0b434bd8c88ff7233ce7b9a4876f3315c22fce7eca1b0 *tini" | sha256sum -c - && \
mv tini /usr/local/bin/tini && \
chmod +x /usr/local/bin/tini
RUN wget https://raw.githubusercontent.com/mpg-age-bioinformatics/draco_pipelines/master/software/newmod.sh \
&& sed -i 's/u\/jboucas\/modules/modules/g' newmod.sh && chmod 777 newmod.sh && mv newmod.sh /usr/bin
ENV MODULEPATH $MODF/bioinformatics:$MODF/general:$MODF/libs
# gsl
RUN cd $SOUR && wget ftp://ftp.gnu.org/gnu/gsl//gsl-2.6.tar.gz && \
mkdir -p $SOFT/gsl/2.6.0 && \
tar -zxvf gsl-2.6.tar.gz && \
cd gsl-2.6 && \
./configure --prefix=$SOFT/gsl/2.6.0 && \
make && \
make install && \
newmod.sh \
-s gsl \
-p $MODF/libs/ \
-v 2.6.0 \
-d 2.6.0 && \
echo "prepend-path LIBRARY_PATH /modules/software/gsl/2.6.0/lib" >> $MODF/libs/gsl/2.6.0 && \
rm -rf $SOUR/*
# bzip2
RUN cd $SOUR && wget https://sourceware.org/pub/bzip2/bzip2-1.0.8.tar.gz && \
tar -xzf bzip2-1.0.8.tar.gz && \
cd bzip2-1.0.8 && \
mkdir -p $SOFT/bzip2/1.0.8 && \
sed -i "18s/.*/CC\=gcc -fPIC/" Makefile && \
make -f Makefile-libbz2_so COMPILE_FLAGS+=-fPIC && make clean && make COMPILE_FLAGS+=-fPIC && \
make -n install PREFIX=$SOFT/bzip2/1.0.8 COMPILE_FLAGS+=-fPIC && make install PREFIX=$SOFT/bzip2/1.0.8 COMPILE_FLAGS+=-fPIC && \
cp -v bzip2-shared $SOFT/bzip2/1.0.8/bin/bzip2 && \
cp -av libbz2.so* $SOFT/bzip2/1.0.8/lib && \
newmod.sh \
-s bzip2 \
-p $MODF/libs/ \
-v 1.0.8 \
-d 1.0.8 && \
rm -rf $SOUR/*
# xz
RUN cd $SOUR && wget http://tukaani.org/xz/xz-5.2.4.tar.gz && \
tar -xzf xz-5.2.4.tar.gz && \
cd xz-5.2.4 && \
mkdir -p $SOFT/xz/5.2.4 && \
./configure --prefix=$SOFT/xz/5.2.4 && make && make install && \
newmod.sh \
-s xz \
-p $MODF/libs/ \
-v 5.2.4 \
-d 5.2.4 && \
rm -rf $SOUR/*
# openblas
RUN cd $SOUR && wget https://github.com/xianyi/OpenBLAS/archive/v0.3.7.tar.gz && \
mv v0.3.7.tar.gz openblas-0.3.7.tar.gz && \
tar -xzf openblas-0.3.7.tar.gz && \
cd OpenBLAS-0.3.7 && \
mkdir -p $SOFT/openblas/0.3.7 && \
make PREFIX=$SOFT/openblas/0.3.7 && \
make install PREFIX=$SOFT/openblas/0.3.7 && \
newmod.sh \
-s openblas \
-p $MODF/libs/ \
-v 0.3.7 \
-d 0.3.7 && \
rm -rf $SOUR/*
# jre
RUN cd $SOUR && wget -O jre-8.0.231-linux-x64.tar.gz https://javadl.oracle.com/webapps/download/AutoDL?BundleId=240718_5b13a193868b4bf28bcb45c792fce896 && \
tar -zxvf jre-8.0.231-linux-x64.tar.gz && \
cd jre1.8.0_231 && \
mkdir -p $SOFT/jre/8.0.231&& \
cp -r * $SOFT/jre/8.0.231/ && \
newmod.sh \
-s jre \
-p $MODF/general/ \
-v 8.0.231 \
-d 8.0.231 && \
echo "setenv JAVA_HOME $SOFT/jre/8.0.231" >> $MODF/general/jre/8.0.231 && \
rm -rf $SOUR/*
# jdk
RUN cd $SOUR && \
wget --no-check-certificate -c --header "Cookie: oraclelicense=accept-securebackup-cookie" https://download.oracle.com/otn-pub/java/jdk/13.0.1+9/cec27d702aa74d5a8630c65ae61e4305/jdk-13.0.1_linux-x64_bin.tar.gz && \
tar -xvzf jdk-13.0.1_linux-x64_bin.tar.gz && \
mkdir -p $SOFT/jdk/13.0.1/bin && \
cd jdk-13.0.1 && \
cp -r * $SOFT/jdk/13.0.1/ && \
newmod.sh \
-s jdk \
-p $MODF/general/ \
-v 13.0.1 \
-d 13.0.1 && \
echo "setenv JAVA_HOME $SOFT/jdk/13.0.1" >> $MODF/general/jdk/13.0.1 && \
rm -rf $SOUR/*
# perl/cpanm
RUN mkdir -p $SOFT/perl/5.28.1/bin && \
cd $SOFT/perl/5.28.1/bin && \
curl -L https://cpanmin.us/ -o cpanm && \
chmod +x cpanm && \
newmod.sh -s perl -p $MODF/general -v 5.28.1 -d 5.28.1 && \
echo 'set home $::env(HOME)' >> $MODF/general/perl/5.28.1 && \
echo 'set perluser $home/.software_container/.perl/5.28.1' >> $MODF/general/perl/5.28.1 && \
echo 'exec /bin/mkdir -p $perluser' >> $MODF/general/perl/5.28.1 && \
echo 'prepend-path PERL5LIB $perluser/lib/perl5' >> $MODF/general/perl/5.28.1 && \
echo 'setenv PERLUSER $perluser' >> $MODF/general/perl/5.28.1
# Install R-3.6.1
RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
module load bzip2/1.0.8 && \
module load xz/5.2.4 && \
module load jdk/13.0.1 && \
cd $SOUR && wget http://ftp5.gwdg.de/pub/misc/cran/src/base/R-3/R-3.6.1.tar.gz && \
tar -xzf R-3.6.1.tar.gz && \
cd R-3.6.1 && \
mkdir -p $SOFT/rlang/3.6.1/bin && \
./configure --prefix=$SOFT/rlang/3.6.1 \
CFLAGS="-I$SOFT/bzip2/1.0.8/include \
-I$SOFT/xz/5.2.4/include \
-I$SOFT/jdk/13.0.1/include" \
LDFLAGS="-L$SOFT/bzip2/1.0.8/lib \
-L$SOFT/xz/5.2.4/lib \
-L$SOFT/jdk/13.0.1/lib" \
--with-cairo=yes --with-libpng=yes \
--with-readline --with-tcltk --enable-R-profiling \
--enable-R-shlib=yes --enable-memory-profiling --with-blas --with-lapack && \
make && make install && \
newmod.sh \
-s rlang \
-p $MODF/general/ \
-v 3.6.1 \
-d 3.6.1 && \
echo "set home $::env(HOME)" >> $MODF/general/rlang/3.6.1 && \
echo "exec /bin/mkdir -p \$home/.software_container/.R/3.6.1/R_LIBS_USER/" >> $MODF/general/rlang/3.6.1 && \
echo "setenv R_LIBS_USER \$home/.software_container/.R/3.6.1/R_LIBS_USER" >> $MODF/general/rlang/3.6.1 && \
echo "prepend-path LD_LIBRARY_PATH $SOFT/rlang/3.6.1/lib/R/lib" >> $MODF/general/rlang/3.6.1 && \
echo "prepend-path CPATH $SOFT/rlang/3.6.1/lib/R/include" >> $MODF/general/rlang/3.6.1 && \
echo "prepend-path C_INCLUDE_PATH $SOFT/rlang/3.6.1/lib/R/include" >> $MODF/general/rlang/3.6.1 && \
echo "prepend-path CPLUS_INCLUDE_PATH $SOFT/rlang/3.6.1/lib/R/include" >> $MODF/general/rlang/3.6.1 && \
echo "prepend-path OBJC_INCLUDE_PATH $SOFT/rlang/3.6.1/lib/R/include" >> $MODF/general/rlang/3.6.1 && \
echo "module load jdk/13.0.1" >> $MODF/general/rlang/3.6.1 && \
echo "setenv CFLAGS \"-I$SOFT/jdk/13.0.1/include -I$SOFT/bzip2/1.0.8/include -I$SOFT/xz/5.2.4/include\"" >> $MODF/general/rlang/3.6.1 && \
echo "setenv LDFLAGS \"-L$SOFT/jdk/13.0.1/lib -L$SOFT/bzip2/1.0.8/lib -L$SOFT/xz/5.2.4/lib\"" >> $MODF/general/rlang/3.6.1' && \
rm -rf ${SOUR}/*
# jupyterhub v2.0.0
RUN cd $SOUR && \
wget https://www.python.org/ftp/python/3.8.0/Python-3.8.0.tgz && \
wget https://www.python.org/ftp/python/2.7.16/Python-2.7.16.tgz && \
tar xzf Python-3.8.0.tgz && \
tar xzf Python-2.7.16.tgz && \
/bin/bash -c 'source /etc/profile.d/modules.sh && \
module load openblas/0.3.7 && \
cd $SOUR/Python-2.7.16 && \
mkdir -p $SOFT/jupyterhub/1.0.0/bin && \
./configure --prefix=$SOFT/jupyterhub/1.0.0 --enable-loadable-sqlite-extensions --enable-shared --with-ensurepip=yes \
CLFAGS="-I$SOFT/openblas/0.3.7/include" \
LDFLAGS="-L$SOFT/openblas/0.3.7/lib" && \
make && make install && \
cd $SOUR/Python-3.8.0 && \
./configure --prefix=$SOFT/jupyterhub/1.0.0 --enable-loadable-sqlite-extensions --enable-shared -with-ensurepip=yes \
CLFAGS="-I$SOFT/openblas/0.3.7/include" \
LDFLAGS="-L$SOFT/openblas/0.3.7/lib" && \
make && make install && \
newmod.sh \
-s jupyterhub \
-p $MODF/general/ \
-v 1.0.0 \
-d 1.0.0 && \
echo "set home $::env(HOME)" >> $MODF/general/jupyterhub/1.0.0 && \
echo "set pythonuser \$home/.software_container/.jupyterhub/1.0.0/bin" >> $MODF/general/jupyterhub/1.0.0 && \
echo "exec /bin/mkdir -p \$pythonuser" >> $MODF/general/jupyterhub/1.0.0 && \
echo "prepend-path PATH \$home/.software_container/.jupyterhub/1.0.0/bin" >> $MODF/general/jupyterhub/1.0.0 && \
echo "set jupyter_runtime_dir \$home/.software_container/.jupyterhub/1.0.0/jupyter/run" >> $MODF/general/jupyterhub/1.0.0 && \
echo "exec /bin/mkdir -p \$jupyter_runtime_dir" >> $MODF/general/jupyterhub/1.0.0 && \
echo "setenv JUPYTER_RUNTIME_DIR \$home/.software_container/.jupyterhub/1.0.0/jupyter/run" >> $MODF/general/jupyterhub/1.0.0 && \
echo "set jupyter_data_dir \$home/.software_container/.jupyterhub/1.0.0/jupyter/data" >> $MODF/general/jupyterhub/1.0.0 && \
echo "exec /bin/mkdir -p \$jupyter_data_dir" >> $MODF/general/jupyterhub/1.0.0 && \
echo "setenv JUPYTER_DATA_DIR \$home/.software_container/.jupyterhub/1.0.0/jupyter/data" >> $MODF/general/jupyterhub/1.0.0 && \
echo "setenv PYTHONHOME $SOFT/jupyterhub/1.0.0/" >> $MODF/general/jupyterhub/1.0.0 && \
echo "setenv PYTHONUSERBASE \$home/.software_container/.jupyterhub/1.0.0/" >> $MODF/general/jupyterhub/1.0.0 && \
echo "exec /bin/mkdir -p \$home/.software_container/.jupyterhub/1.0.0/pythonpath/site-packages" >> $MODF/general/jupyterhub/1.0.0 && \
echo "module load openblas/0.3.7 rlang/3.6.1" >> $MODF/general/jupyterhub/1.0.0 && \
module load jupyterhub/1.0.0 && \
pip3 install jupyter && \
python2 -m pip install ipykernel && \
python2 -m ipykernel install' && \
rm -rf ${SOUR}/*
## Libraries required for jupyter R kernel
RUN echo "install.packages('askpass', repos='http://cran.us.r-project.org')" > $SOUR/askpass.install.R && \
echo "install.packages(c('repr', 'IRdisplay', 'evaluate', 'crayon', 'pbdZMQ', 'devtools', 'uuid', 'digest'), lib=c('$SOFT/rlang/3.6.1/lib/R/library') ,repos=c('http://ftp5.gwdg.de/pub/misc/cran/'), dependencies=TRUE )" > $SOUR/jupyter.install.R && \
echo "devtools::install_github('IRkernel/IRkernel',lib=c('$SOFT/rlang/3.6.1/lib/R/library')) " >> $SOUR/_jupyter.install.R && \
echo "IRkernel::installspec(name = 'ir361', displayname = 'R 3.6.1')" > $SOUR/.install.jupyter.R.kernel.3.6.1
RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
module load jupyterhub && \
module load rlang && \
cd $SOUR && \
$SOFT/rlang/3.6.1/bin/Rscript $SOUR/askpass.install.R && \
wget -O openssl_1.3.0.tar.gz https://github.com/jeroenooms/openssl/archive/v1.3.0.tar.gz && \
$SOFT/rlang/3.6.1/bin/R CMD INSTALL -l $SOFT/rlang/3.6.1/lib/R/library openssl_1.3.0.tar.gz && \
git clone https://github.com/ropensci/git2r.git && \
$SOFT/rlang/3.6.1/bin/R CMD INSTALL -l $SOFT/rlang/3.6.1/lib/R/library git2r && \
$SOFT/rlang/3.6.1/bin/Rscript $SOUR/jupyter.install.R && \
$SOFT/rlang/3.6.1/bin/Rscript $SOUR/_jupyter.install.R && \
Rscript $SOUR/.install.jupyter.R.kernel.3.6.1 && rm $SOUR/jupyter.install.R $SOUR/_jupyter.install.R $SOUR/.install.jupyter.R.kernel.3.6.1' && \
rm -rf ${SOUR}/*
## Finished installation of jupyter R kernel
## Install rstudio server ##
RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
module load jupyterhub && \
module load rlang && \
cd ${SOUR} && \
wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.5019-amd64.deb && \
dpkg -i rstudio-server-1.2.5019-amd64.deb && \
echo "rsession-which-r=$(which R)" >> /etc/rstudio/rserver.conf' && \
rm -rf ${SOUR}/*
RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
module load jre && \
mkdir -p $SOFT/cytoscape/3.7.2 && \
cd $SOFT/cytoscape/3.7.2 && wget https://github.com/cytoscape/cytoscape/releases/download/3.7.2/Cytoscape_3_7_2_unix.sh && \
bash Cytoscape_3_7_2_unix.sh -q && \
newmod.sh \
-s cytoscape \
-p $MODF/bioinformatics/ \
-v 3.7.2 \
-d 3.7.2 && \
echo "module load jre" >> $MODF/bioinformatics/cytoscape/3.7.2 && \
echo "prepend-path PATH /usr/local/Cytoscape_v3.7.2" >> $MODF/bioinformatics/cytoscape/3.7.2' && \
rm -rf ${SOUR}/*
USER $NB_USER
RUN mkdir /home/$NB_USER/py2cytoscape
# COPY * /home/$NB_USER/py2cytoscape
# RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
# module load jupyterhub && \
# cd py2cytoscape && \
# python3 setup.py develop --user'
##########################
#### this part to end ####
##########################
# Jupyter port
EXPOSE 8888
# rstudio server port
EXPOSE 8787
COPY .bashrc /home/$NB_USER/.bashrc
RUN echo "options(bitmapType='cairo')" > /home/$NB_USER/.Rprofile
RUN mkdir -p /home/$NB_USER/.software_container/.jupyter
COPY jupyter_notebook_config.py /home/$NB_USER/.software_container/.jupyter/
USER root
# Folders in home folder that should be kept
ENV HOFOL ".bashrc .bash_logout .Rprofile .software_container"
RUN for i in $(ls /home/mpiage/) ; do echo ${i}; done
RUN mkdir -p /home/_mpiage \
&& for f in $HOFOL ; do \
if [ ! -e /home/mpiage/${f} ] ;\
then echo 'no ${f}..' ;\
else cp -rv /home/mpiage/${f} /home/_mpiage/; \
fi \
done
ENTRYPOINT /bin/bash -c '\
for f in $HOFOL ; do \
if [[ ! -e /home/mpiage/${f} ]] ; \
then cp -vr /home/_mpiage/${f} /home/mpiage/${f}; \
fi \
done \
&& source /home/mpiage/.bashrc \
&& /bin/bash'
WORKDIR /home/mpiage
RUN chown -R mpiage: /home/mpiage
RUN mkdir -p /Dockerfiles/v3.0.0s
COPY Dockerfile /Dockerfiles/v3.0.0s/
USER $NB_USER