diff --git a/_reader/RNAseqWorkshop.pdf b/_reader/RNAseqWorkshop.pdf
index 4226a0ca38dd8de51b23e8a3b8de6d06207dc19d..db4b03f863bce1a9f179c1f611bf3a5e91616349 100644
Binary files a/_reader/RNAseqWorkshop.pdf and b/_reader/RNAseqWorkshop.pdf differ
diff --git a/workflows/maindocker/Dockerfile b/workflows/maindocker/Dockerfile
index 79e8ee8574dff05c79c59eea66acc04f3295c2c7..c7d356ad6c017229d9e601add6747f43bd9963a1 100644
--- a/workflows/maindocker/Dockerfile
+++ b/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
 
diff --git a/workflows/maindocker/python_installs.sh b/workflows/maindocker/python_installs.sh
index 9b81259d4c6002dca4f275c657e678ecfa2df026..88783ad1382db1ded9ec1a1c74c65a3f323cf6bd 100755
--- a/workflows/maindocker/python_installs.sh
+++ b/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