day three as ready as it's getting

workflows/maindocker/Dockerfile

@@ -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
 
-WORKDIR /home/$DOCKER_USER/repos
-RUN git clone https://github.com/alisandra/RNAseq_workshop_helpers.git
-RUN mkdir /home/$DOCKER_USER/bin && find RNAseq_workshop_helpers . -maxdepth 2 -type f -executable|xargs -I% cp % /home/$DOCKER_USER/bin/
+RUN mkdir /home/$DOCKER_USER/repos && \
+  cd /home/$DOCKER_USER/repos && \
+  git clone https://github.com/alisandra/RNAseq_workshop_helpers.git && \
+  mkdir /home/$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 'export PATH=$PATH:'$SOFTWAREDIR'/bin'
@@ -117,6 +119,9 @@ EXPOSE 8889
 COPY ./first.sh /home/$DOCKER_USER/ 
 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}"
 USER $DOCKER_USER
 

workflows/maindocker/python_installs.sh

@@ -24,7 +24,6 @@ cd repos/alisandra
 git clone https://github.com/Magdoll/cDNA_Cupcake.git
 cd cDNA_Cupcake/
 git checkout v28.0.0
-pip3 install -r requirements.txt
 pip install .
 cd $oldpwd