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Commit d10d8f18 authored by Alisandra Denton's avatar Alisandra Denton
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day three as ready as it's getting

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...@@ -24,9 +24,11 @@ ENV TZ=Europe/Berlin ...@@ -24,9 +24,11 @@ ENV TZ=Europe/Berlin
RUN apt install libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev cmake jellyfish python-tk libcurl4-openssl-dev libgit2-dev libssl-dev -y RUN apt install libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev cmake jellyfish python-tk libcurl4-openssl-dev libgit2-dev libssl-dev -y
WORKDIR /home/$DOCKER_USER/repos RUN mkdir /home/$DOCKER_USER/repos && \
RUN git clone https://github.com/alisandra/RNAseq_workshop_helpers.git cd /home/$DOCKER_USER/repos && \
RUN mkdir /home/$DOCKER_USER/bin && find RNAseq_workshop_helpers . -maxdepth 2 -type f -executable|xargs -I% cp % /home/$DOCKER_USER/bin/ git clone https://github.com/alisandra/RNAseq_workshop_helpers.git && \
mkdir /home/$DOCKER_USER/bin && \
find RNAseq_workshop_helpers . -maxdepth 2 -type f -executable|xargs -I% cp % /home/$DOCKER_USER/bin/
#echo "please add the following lines to your ~/.bashrc file" #echo "please add the following lines to your ~/.bashrc file"
#echo 'export PATH=$PATH:'$SOFTWAREDIR'/bin' #echo 'export PATH=$PATH:'$SOFTWAREDIR'/bin'
...@@ -117,6 +119,9 @@ EXPOSE 8889 ...@@ -117,6 +119,9 @@ EXPOSE 8889
COPY ./first.sh /home/$DOCKER_USER/ COPY ./first.sh /home/$DOCKER_USER/
RUN chown $DOCKER_USER:$DOCKER_USER /home/$DOCKER_USER/first.sh RUN chown $DOCKER_USER:$DOCKER_USER /home/$DOCKER_USER/first.sh
RUN cd /home/$DOCKER_USER/repos/alisandra/cDNA_Cupcake && \
pip install .
ENV PATH="/home/$DOCKER_USER/bin:${PATH}" ENV PATH="/home/$DOCKER_USER/bin:${PATH}"
USER $DOCKER_USER USER $DOCKER_USER
......
...@@ -24,7 +24,6 @@ cd repos/alisandra ...@@ -24,7 +24,6 @@ cd repos/alisandra
git clone https://github.com/Magdoll/cDNA_Cupcake.git git clone https://github.com/Magdoll/cDNA_Cupcake.git
cd cDNA_Cupcake/ cd cDNA_Cupcake/
git checkout v28.0.0 git checkout v28.0.0
pip3 install -r requirements.txt
pip install . pip install .
cd $oldpwd cd $oldpwd
......
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