diff --git a/Dockerfile b/Dockerfile
index c3dc4060..699d26d1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -10,10 +10,11 @@ MAINTAINER Kendell Clement
 RUN apt-get update && apt-get install gcc g++ bowtie2 samtools libsys-hostname-long-perl \
   -y --no-install-recommends \
   && apt-get clean \
+  && apt-get autoremove -y \
   && rm -rf /var/lib/apt/lists/* \
   && rm -rf /usr/share/man/* \
   && rm -rf /usr/share/doc/* \
-  && conda install -c defaults -c conda-forge -c bioconda -y -n base --debug fastp numpy cython jinja2 tbb=2020.2 pyparsing=2.3.1 scipy matplotlib-base pandas plotly\
+  && conda install -c defaults -c conda-forge -c bioconda -y -n base --debug trimmomatic flash numpy cython jinja2 tbb=2020.2 pyparsing=2.3.1 scipy matplotlib-base pandas plotly\
   && conda clean --all --yes
 
 #install ms fonts
@@ -32,7 +33,7 @@ RUN echo "deb http://httpredir.debian.org/debian buster main contrib" > /etc/apt
 # install crispresso
 COPY . /CRISPResso2
 WORKDIR /CRISPResso2
-RUN python setup.py install
+RUN python setup.py install \
   && CRISPResso -h \
   && CRISPRessoBatch -h \
   && CRISPRessoPooled -h \