# Building Jalview from Source

## tl;dr

```
# download
git clone http://source.jalview.org/git/jalview.git
# compile
cd jalview
gradle shadowJar
# run
java -jar build/libs/jalview-all-11.jar

# and/or create launcher
gradle getdown
# use launcher
cd getdown/files
java -jar getdown-launcher.jar . jalview
```


## What you will need

The method here is described in terms of using a command line.  You can easily do this on linux or in a Terminal window in macOS.  You can do it in Windows.

* Java 11 compliant JDK
* gradle 5.1 or above
* git

### Java 11 JDK
We recommend obtaining an OpenJDK JDK 11 (since 11 is the long term support release) from AdoptOpenJDK: <https://adoptopenjdk.net/?variant=openjdk11&jvmVariant=hotspot>, either the *Installer* or `.zip`/`.tar.gz` variants whichever you prefer (if you're not sure, choose the *Installer*).

### 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/>.
After installing `brew`, open a Terminal window and type in (using an Administrator privileged user):

```
brew install gradle git
```

or

```
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

```
 sudo apt-get install gradle git
```

##### for RPM-based distributions (e.g. Fedora, CentOS, RedHat)
run

```
sudo yum install gradle git
```

If you have some other version of linux you'll probably be able to work it out!


#### 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`.
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.






and then you can build the Jalview jar file using gradle.