The environment is now set up by Docker

docker/Dockerfile

 # This is a Dockerfile to run eHive scripts (init_pipeline.pl, beekeeper.pl, runWorker.pl) in a container
 #
+## Build the image
 # docker build -t ensembl-hive .
 #
-# docker run -it -e PATH=/repo/ensembl-hive/scripts:/bin:/usr/bin:/usr/local/bin:/sbin:/usr/sbin:/usr/local/sbin ensembl-hive		# assume bash 
-# docker run -it -e PATH=/repo/ensembl-hive/scripts:/bin:/usr/bin:/usr/local/bin:/sbin:/usr/sbin:/usr/local/sbin ensembl-hive init_pipeline.pl Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMult_conf -pipeline_url $URL
-# docker run -it -e PATH=/repo/ensembl-hive/scripts:/bin:/usr/bin:/usr/local/bin:/sbin:/usr/sbin:/usr/local/sbin ensembl-hive beekeeper.pl -url $URL -loop -sleep 0.2
-# docker run -it -e PATH=/repo/ensembl-hive/scripts:/bin:/usr/bin:/usr/local/bin:/sbin:/usr/sbin:/usr/local/sbin ensembl-hive runWorker.pl -url $URL
+## Open a session in a new container (will run bash)
+# docker run -it ensembl-hive
+#
+## Initialize and run a pipeline
+# docker run -it ensembl-hive init_pipeline.pl Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMult_conf -pipeline_url $URL
+# docker run -it ensembl-hive beekeeper.pl -url $URL -loop -sleep 0.2
+# docker run -it ensembl-hive runWorker.pl -url $URL
 
 
 FROM ubuntu:16.04
@@ -33,7 +37,7 @@ RUN mkdir /repo && git clone -b master https://github.com/Ensembl/ensembl-hive.g
 # Install the missing dependencies (if any)
 RUN cpanm --installdeps --with-recommends /repo/ensembl-hive
 
-	# for the processes you run in an interactive bash
-RUN echo "export PATH=$PATH:/repo/ensembl-hive/scripts" >>/root/.bashrc
+ENV PATH "/repo/ensembl-hive/scripts:$PATH"
+ENV PERL5LIB "/repo/ensembl-hive/modules:$PERL5LIB"
 
 CMD [ "/bin/bash" ]