From 32b479a4470b0b331f805843981415a7130c8b8e Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Tue, 28 May 2019 10:50:32 +0100
Subject: [PATCH] JAL-3248 saving

---
 doc/building.md |   54 +++++++++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 47 insertions(+), 7 deletions(-)

diff --git a/doc/building.md b/doc/building.md
index e410469..b5d8114 100644
--- a/doc/building.md
+++ b/doc/building.md
@@ -14,7 +14,8 @@ We recommend obtaining an OpenJDK JDK 11 from AdoptOpenJDK: <https://adoptopenjd
 ### gradle and git
 You should be able to install the latest (or close to the latest) versions of gradle and git using your OS package manager.
 
-For **macOS** we recommend using `brew`, which can be installed following the instructions at <https://brew.sh/>.
+#### For **macOS**
+we recommend using `brew`, which can be installed following the instructions at <https://brew.sh/>.
 After installing `brew`, open a Terminal window and type in (using an Administrator privileged user):
 
 ```
@@ -29,14 +30,18 @@ brew upgrade gradle git
 
 if you already have them installed but need to upgrade the version.
 
-For **linux** this will depend on which distribution you're using.
-For *Debian* based distributions (e.g. Mint, Ubuntu, Debian) run
+#### For **linux**
+this will depend on which distribution you're using.
+
+##### For *Debian* based distributions (e.g. Mint, Ubuntu, Debian)
+run
 
 ```
  sudo apt-get install gradle git
 ```
 
-whilst for RPM-based distributions run (probably)
+##### for RPM-based distributions (e.g. Fedora, CentOS, RedHat)
+run (probably)
 
 ```
 sudo yum install gradle git
@@ -44,13 +49,48 @@ sudo yum install gradle git
 
 If you have some other version of linux you'll probably be able to work it out!
 
-For **Windows** users, you will likely do well by using the **Chocolatey** package manager.  See install instructions at <https://chocolatey.org/>, and you will just need
+
+#### For **Windows**
+
+we suggest using the **Chocolatey** package manager.  See install instructions at <https://chocolatey.org/>, and you will just need
 
 ```
 choco install gradle git
 ```
 
 Alternatively, you could install a real `bash` shell and install both `gradle` and `git` through `apt-get`.
-Another alternative would be to install them separately following the instructions at <https://gradle.org/install/>, and for `git` here are a couple of suggestions: Git for Windows <https://gitforwindows.org/> or a real `bash`-shell <https://devblogs.microsoft.com/commandline/bash-on-ubuntu-on-windows-download-now-3/> !
+See <https://devblogs.microsoft.com/commandline/bash-on-ubuntu-on-windows-download-now-3/> 
+for how to install the ubuntu bash shell in Windows 10.
+
+Another alternative would be to install them separately. For `gradle` follow the instructions at <https://gradle.org/install/>, and for `git` here are a couple of suggestions: Git for Windows <https://gitforwindows.org/>.
+
+## Downloading the Jalview source tree
+
+This can be done with `git`.
+On the command line, change directory to where you want to download Jalview's build-tree 
+top level directory.  Then run
+
+```
+git clone http://source.jalview.org/git/jalview.git
+```
+
+You'll get some progress output and after a minute or two you should have the full 
+Jalview build-tree in the folder `jalview`.
+
+## What's in the source tree?
+
+Change directory into the `jalview` folder:
+
+```
+cd jalview
+```
+and you'll find most of the Jalview source files under `src`. Some important resource 
+files can be found under `resources`.  The helper jar libraries can currently be found 
+in `j8lib` for Java 1.8 runtime and `j11lib` for Java 11 runtime.
+
+
+
+
+
 
-##
\ No newline at end of file
+and then you can build the Jalview jar file using gradle.
\ No newline at end of file
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