ApolloRNA: downloading and installing

ApolloRNA is supported on Windows, MAC OS X and Linux type platforms.
Note that the installation requires to install several softwares: Apollo, convert from the ImageMagick package, RNAfold and RNAeval from the Vienna RNA package.
Administrator access is required to easily install ImageMagick on your computer.

A download and install protocol is described on Nature Protocols Networks.
Below, a short description is also provided for the considered platforms:

WINDOWS instructions
MAC OS X instructions
LINUX instructions

Go to the Apollo download page, download installer for Windows (which includes Java VM) and follow installation instructions.
Under the Apollo root directory, in the jars directory, rename apollo.jar to apollo.jar.save.
Go to the ApolloRNA download page and download the file apollo.jar in the Apollo root directory.
Save the files RNAfold.exe and RNAeval.exe in the Apollo root directory.
Configure environment variable Path :
- On the desktop, click Start, click Control Panel, (For Windows XP Professionnal users, click Performance and Maintenance), and then click System.
- On the Advanced tab, click Environment Variables.
- If the User variable 'Path' exists:
  Select 'Path', click edit and add at the end of the value line ";"+way of the Apollo root directory.
  For instance, if the Apollo root directory is C:\Documents and Settings\dupont\Apollo, add the text:
```
;C:\Documents and Settings\dupont\Apollo
```
  Else:
  Click add, create a variable named 'Path' and affect it the value way of the Apollo root directory.
  For instance, if the Apollo root directory is C:\Documents and Settings\dupont\Apollo, affect the text:
```
C:\Documents and Settings\dupont\Apollo
```
Install ImageMagick for Windows
- Go to ImageMagick page.
- Download the appropriated executable file.
- Execute it.
Install Ghostscript
- Go to ghostscript download page.
- In the part "File Releases", in subpart "AFPL Ghostscript", download gs854w32.exe.
- Execute it.

To launch ApolloRNA: in the Apollo root directory, click the Apollo icon.

Go to the Apollo download page, download installer for WindowsMAC OS X and follow installation instructions.
Check if SUN Java1.5 is installed on your computer. (To know the java version, open a shell and at the prompt, type: java -version)
If Java1.5 isn't installed, go to Apple's instructions on how to do this, using Software Updates.
Configure Apollo for Java
- Open a shell and at the prompt, type: which java
  The displayed line is for instance "/usr/bin/java"
- In the Apollo root directory, in the subdirectory conf, open apollo.cfg and add for instance the line:
```
JavaPath		"/usr/"
```
Undet the Apollo root directory, in the jars directory, rename apollo.jar to apollo.jar.save.
Go to the ApolloRNA download page and download the file apollo.jar in the Apollo root directory.
Install the Vienna RNA package (which included RNAfold et RNAeval)
- Go to the main page of the Vienna RNA Package.
- Click 'source distribution here' link and save the ViennaRNA gz file.
- To install the Vienna RNA package, follow instructions here.
Install ImageMagick
- Download ImageMagick.tar.gz and save it in your Applications directory.
- Open a shell and go (command cd) to the Applications directory.
- Follow the Unix installation instructions.
Install Ghostscript
- Go to Ghostscript download page.
- In part "File Releases", in subpart "AFPL Ghostscript", download ghostscript-8.54.tar.gz in your Applications directory.
- To unpack it, open a shell and go to the Applications directory.
  At the prompt, type: tar xzvf ghostscript-8.54.tar.gz
- To install Ghostscript, type:
  cd ghostscript-8.54 ./configure make make install

To launch ApolloRNA: open a shell, go to the Apollo root directory and type: apollo

Go to the Apollo download page, download installer for Linux (which includes Java VM) and follow installation instructions..
Under the Apollo root directory, in thr jars directory, rename apollo.jar to apollo.jar.save.
Go to the ApolloRNA download page and download the file apollo.jar in the Apollo root directory.
Install the Vienna RNA package (which included RNAfold et RNAeval)
- Go to the main page of Vienna RNA Package.
- Click 'source distribution here' link and save the ViennaRNA gz file.
- To install the Vienna RNA package, follow instructions here.
Install ImageMagick
- Download ImageMagick.tar.gz.
- Open a shell and go to the directory where the file was downloaded.
- Follow the Unix installation instructions.
Install Ghostscript
- Go to Ghostscript download page.
- In part "File Releases", in subpart "AFPL Ghostscript", download ghostscript-8.54.tar.gz.
- To unpack it, open a shell and go to the directory where the file was downloaded.
  At the prompt, type: tar xzvf ghostscript-8.54.tar.gz
- To install Ghostscript, type:
  cd ghostscript-8.54 ./configure make make install

To launch ApolloRNA: open a shell, go to the Apollo root directory and type: apollo