Change master to version/2.5 in references

README.md

 eHive
 =====
 
-[![Travis Build Status](https://travis-ci.org/Ensembl/ensembl-hive.svg?branch=master)](https://travis-ci.org/Ensembl/ensembl-hive)
-[![Coverage Status](https://coveralls.io/repos/Ensembl/ensembl-hive/badge.svg?branch=master&service=github)](https://coveralls.io/github/Ensembl/ensembl-hive?branch=master)
-[![Documentation Status](https://readthedocs.org/projects/ensembl-hive/badge/?version=master)](http://ensembl-hive.readthedocs.io/en/master)
-[![codecov](https://codecov.io/gh/Ensembl/ensembl-hive/branch/master/graph/badge.svg)](https://codecov.io/gh/Ensembl/ensembl-hive/branch/master)
+[![Travis Build Status](https://travis-ci.org/Ensembl/ensembl-hive.svg?branch=version/2.5)](https://travis-ci.org/Ensembl/ensembl-hive)
+[![Coverage Status](https://coveralls.io/repos/Ensembl/ensembl-hive/badge.svg?branch=version/2.5&service=github)](https://coveralls.io/github/Ensembl/ensembl-hive?branch=version/2.5)
+[![Documentation Status](https://readthedocs.org/projects/ensembl-hive/badge/?version=version-2.5)](http://ensembl-hive.readthedocs.io/en/version-2.5)
+[![codecov](https://codecov.io/gh/Ensembl/ensembl-hive/branch/version%2F2.5/graph/badge.svg)](https://codecov.io/gh/Ensembl/ensembl-hive/branch/version%2F2.5)
 [![Code Climate](https://codeclimate.com/github/Ensembl/ensembl-hive/badges/gpa.svg)](https://codeclimate.com/github/Ensembl/ensembl-hive)
 [![Docker Build Status](https://img.shields.io/docker/build/ensemblorg/ensembl-hive.svg)](https://hub.docker.com/r/ensemblorg/ensembl-hive)
 
@@ -16,7 +16,7 @@ Available documentation
 -----------------------
 
 The main entry point is available online in the [user
-manual](https://ensembl-hive.readthedocs.io/en/master/), from where it can
+manual](https://ensembl-hive.readthedocs.io/en/version-2.5/), from where it can
 be downloaded for offline access.
 
 
@@ -74,7 +74,7 @@ eHive has a generic interface named _Meadow_ that describes how to interact with
 Sun Grid Engine (now known as Oracle Grid Engine),
 [HTCondor](https://research.cs.wisc.edu/htcondor/),
 [PBS Pro](http://www.pbspro.org),
-[Docker Swarm](https://docs.docker.com/engine/swarm/) and maybe others. Read more about this on [the user manual](http://ensembl-hive.readthedocs.io/en/master/contrib/alternative_meadows.html).
+[Docker Swarm](https://docs.docker.com/engine/swarm/) and maybe others. Read more about this on [the user manual](http://ensembl-hive.readthedocs.io/en/version-2.5/contrib/alternative_meadows.html).
 
 Docker image
 ------------
@@ -106,7 +106,7 @@ Docker Swarm orchestrator, and thus on any cloud infrastructure that supports
 it (e.g. [Amazon Web Services](https://docs.docker.com/docker-cloud/cloud-swarm/create-cloud-swarm-aws/),
 [Microsoft Azure](https://docs.docker.com/docker-cloud/cloud-swarm/create-cloud-swarm-azure/)).
 
-Read more about this on [the user manual](http://ensembl-hive.readthedocs.io/en/master/contrib/docker-swarm.html).
+Read more about this on [the user manual](http://ensembl-hive.readthedocs.io/en/version-2.5/contrib/docker-swarm.html).
 
 Contact us (mailing list)
 -------------------------

docker/Dockerfile

@@ -22,7 +22,7 @@ ARG DEBIAN_FRONTEND=noninteractive
 RUN apt-get update -y && apt-get install -y git && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Clone the repo
-RUN mkdir /repo && git clone -b master https://github.com/Ensembl/ensembl-hive.git /repo/ensembl-hive
+RUN mkdir /repo && git clone -b version/2.5 https://github.com/Ensembl/ensembl-hive.git /repo/ensembl-hive
 
 # Install all the dependencies
 RUN /repo/ensembl-hive/docker/setup_os.Ubuntu-16.04.sh \

docs/rtd_upgrade.sh

@@ -29,8 +29,8 @@ echo http://archive.ubuntu.com/ubuntu/pool/main/libd/libdbi-perl/libdbi-perl_1.6
 mkdir ../root
 for i in *.deb; do dpkg -x "$i" ../root/; done
 
-git clone --branch master --depth 1 https://github.com/Ensembl/ensembl.git ../ensembl
-git clone --branch master --depth 1 https://github.com/Ensembl/ensembl-hive-docker-swarm.git ../ensembl-hive-docker-swarm
+git clone --branch version/2.5 --depth 1 https://github.com/Ensembl/ensembl.git ../ensembl
+git clone --branch version/2.5 --depth 1 https://github.com/Ensembl/ensembl-hive-docker-swarm.git ../ensembl-hive-docker-swarm
 
 rm -f ../../../contrib/docker-swarm
 ln -s "$1/ensembl-hive-docker-swarm/docs" ../../../contrib/docker-swarm