formatting

docs/get-started/create-your-mine.rst

@@ -1,30 +1,30 @@
 Create Your InterMine!
 ==============================
 
-This guide will show you how to create a new InterMine.
-
-You will need all the dependencies listed in :doc:`/system-requirements/software/index.rst`
+This guide will show you how to create a new InterMine. You will need all the dependencies listed in :doc:`</system-requirements/software/index.rst>`
 
 .. note::
 
-    These instructions assume you have taken the :doc:`/get-started/tutorial/index.rst`, a detailed guide to integrating data with InterMine.
+    These instructions assume you have taken the :doc:`</get-started/tutorial/index.rst>`, a detailed guide to integrating data with InterMine.
 
 1. Run a script to create your InterMine
 ----------------------------------------
 
 Download the script.
 
 ::
+
     ~/git/ $ git clone https://github.com/intermine/intermine-scripts.git
 
 Execute the script to generate your InterMine instance
 
 ::
+
     ~/git/ $ ~/git/scripts/make_mine TigerMine
 
 You will see a message like: "created /home/$USER/git/tigermine directory for tigermine"
 
-You now have an InterMine! The :doc:`/get-started/tutorial tutorial` goes into detail about the various files that comprise an InterMine.
+You now have an InterMine! The :doc:`tutorial </get-started/tutorial/index.rst` goes into detail about the various files that comprise an InterMine.
 
 2. Add a mine properties file
 ------------------------------
@@ -54,7 +54,7 @@ Rename the file to match your Mine.
 
 Now update your new properties files with the values correct for your InterMine. 
 
-See :doc:`/webapp/properties/intermine-properties.rst` for details on this file and what each property means.
+See :doc:`</webapp/properties/intermine-properties.rst>` for details on this file and what each property means.
 
 3. Create databases
 --------------------------
@@ -84,11 +84,11 @@ These databases are empty. We'll populate the main database in the following ste
 
 The data loaded into your mine is controlled by the `project.xml` file located in the root of your mine directory.
 
-See :doc:`/database/database-building/project-xml/index.rst` for details on the project XML file. 
+See :doc:`</database/database-building/project-xml/index.rst>` for details on the project XML file. 
 
-InterMine has a few dozen libraries for popular data sources. See :doc:`/database/data-sources/library/index.rst` for the full list. Select one of the data sources and add it to your project XML file.
+InterMine has a few dozen libraries for popular data sources. See :doc:`</database/data-sources/library/index.rst>` for the full list. Select one of the data sources and add it to your project XML file.
 
-For example, :doc:`/database/data-sources/library/ncbi-gene.rst` loads gene information from the NCBI. Download the data files listed, then add the given project XML entry to your own mine's project XML file, like so:
+For example, :doc:`</database/data-sources/library/ncbi-gene.rst>` loads gene information from the NCBI. Download the data files listed, then add the given project XML entry to your own mine's project XML file, like so:
 
 ::
 
@@ -106,7 +106,7 @@ For example, :doc:`/database/data-sources/library/ncbi-gene.rst` loads gene info
     <post-processing/>
     </project>
 
-For details on writing your own data source, see :doc:`/database/data-sources/custom/index.rst`
+For details on writing your own data source, see :doc:`</database/data-sources/custom/index.rst>`
 
 You can also add postprocesses to your build, here are common ones: 
 
@@ -121,12 +121,12 @@ You can also add postprocesses to your build, here are common ones:
   </post-processing>
   
 
-See :doc:`/database/database-building/post-processing/index.rst` for details on what postprocesses do.
+See :doc:`</database/database-building/post-processing/index.rst>` for details on what postprocesses do.
 
 5. Set up your search index (optional)
 ---------------------------------------
 
-Solr handles the keyword search in InterMine. See :doc:`/system-requirements/software/solr.rst` for details on how to set this up for your mine.
+Solr handles the keyword search in InterMine. See :doc:`</system-requirements/software/solr.rst>` for details on how to set this up for your mine.
 
 If you skip this step, your mine will work fine but the keyword search will fail.
 
@@ -138,7 +138,7 @@ Now run the build!
 ::
     ~/git/tigermine $ ./project_build localhost /data/tigermine-build
 
-See :doc:`/database/database-building/build-script.rst` for more on the `project_build` script.
+See :doc:`</database/database-building/build-script.rst>` for more on the `project_build` script.
 
 Deploy your webapp. Make sure tomcat is running.
 
@@ -147,15 +147,15 @@ Deploy your webapp. Make sure tomcat is running.
     # if you have already deployed once, you will want to 
     ~/git/tigermine $ ./gradlew cargoRedeployRemote 
 
-See :doc:`/system-requirements/software/gradle/index.rst` for more on Gradle.
+See :doc:`</system-requirements/software/gradle/index.rst>` for more on Gradle.
 
 Next steps
 ----------------------------
 
 Congratulations! Next you will want to:
 
-* :doc:`/webapp/properties/index.rst customise your mine` 
-* :doc:`/database/data-sources/custom/index.rst add your own data sources` 
-* :doc:`/support/mailing-list.rst join the intermine mailing list`
+* :doc:`</webapp/properties/index.rst> customise your mine` 
+* :doc:`</database/data-sources/custom/index.rst> add your own data sources` 
+* :doc:`</support/mailing-list.rst> join the intermine mailing list`
 
 .. index:: Getting started, make_mine