diff --git a/docker/base/Dockerfile b/docker/base/Dockerfile
index 1db104a..d51bd8a 100644
--- a/docker/base/Dockerfile
+++ b/docker/base/Dockerfile
@@ -40,6 +40,7 @@ ENV PATH $PATH:$JAVA_HOME/bin
 # this is not the ideal way to install all these tools, but the code is currently shared by non-docker usages
 RUN svn co --username cpas --password cpas --no-auth-cache https://hedgehog.fhcrc.org/tor/stedi/branches/${SVN_BRANCH}/externalModules/labModules/SequenceAnalysis/pipeline_code ${LK_HOME}/svn/
 RUN ${LK_HOME}/svn/sequence_tools_install.sh -d ${LK_HOME}
+RUN rm -Rf ${LK_HOME}/tool_src
 
 # Clean up
 RUN rm -rf /var/lib/apt/lists/*