Appion

h1. Quick Install of Appion and Leginon using the auto-installation tool

This quick installation script installs both Appion and Leginon on a single computer running the CentOS 6 Linux operating system. This is not really intended for production systems but is instead perhaps a useful way to evaluate the software prior to undertaking a more complex installation across multiple CPU's. Please note that the auto-installation is intended for use with a clean installation of CentOS 6 and might fail if you already have several other packages installed.  

Follow the instructions below to install Appion and Leginon using the auto-installation script.

# "Install CentOS":http://emg.nysbc.org/projects/appion/wiki/Instructions_for_installing_CentOS_on_your_computer. 

 *Disable SELinux during the installation.* You can check to see if it is enabled after the centOS installation with:

<pre>

/usr/sbin/selinuxenabled

echo $?

</pre>

 If SELinux is enabled, the return value is 0. If it is disabled, the return value is 1.  If you need to disable SELinux, follow the instructions for disabling SELinux found in the troubleshooting section of this document.

 The Auto-Installer currently assumes that you have a fresh centOS installation and that you have not set up a mysql database.

 

# Login to CentOS as the root user. Note that there seems to be an "issue":http://stackoverflow.com/questions/1421498/linux-gedit-i-always-get-gconf-error-failed-to-contact-configuration-server with using su to become root user which prevents the autoinstaller from running to completion.  

 

# [[Appion:Regkey_request|Request a registration key]] which will be needed during installation. We ask that you register so that we can inform the owners of processing packages such as EMAN, XMIPP and SPIDER how many people are recieving their software from us. These numbers help them gain funding to maintain the software.

   

# Download "centosAutoInstallation.py":http://emg.nysbc.org/projects/appion/repository/revisions/myami-3.2/raw/install/centosAutoInstallation.py

http://emg.nysbc.org/projects/leginon/repository/revisions/myami-3.2/raw/install/centosAutoInstallation.py

# Open a Terminal, go to the download directory and run:

<pre>

python centosAutoInstallation.py

</pre>

# Enter an administrator's email address, and root password when prompted. 

 

# You may choose to install several of the third party software packages that Appion uses for image processing. If you do not allow the installer to install them at this time, you can follow the manual installation instructions found toward the end of this page.

 

# Wait. Depending on how many packages are updated during _yum update_, installation could take anywhere between 6 minutes and 2 hours. 

 

# When the installation completes:

## A log file will be created called installation.log. You may want to view it and look for any errors.

## The Leginon start page will be displayed. This indicates that Leginon python components are installed correctly.

## A web browser will be launched with the Appion and Leginon tools loaded.  A few initialization happens in there and then the home page appears if everything works out.

 

# There are some additional changes that need to be made at this point. 

## Please follow the directions for [[appion:Additional Database Server Setup After Web Server Installation]]

{{include(testing auto-installation)}}

h1. Troubleshooting

h2. Having trouble with autoinstaller in general when CentOS is not fresh.

The autoinstaller assumes a fresh CentOS installation.  If some of the previously installed packages had dependency that conflict with what Appion/Leginon uses, problems may occur.

In this case, we suggest run the steps individually to see if you can identify the real problem.  We have a user reported that just by performing them step-by-step, ti worked out for unknown reason.

h2. SELinux is Enabled

If your installation completes and you see a Welcome to Leginon window, a second Leginon window that appears blank and a web page with the Web Tools Setup wizard in a System updating state as shown below, you have installed CentOs with Security Enhanced Linux enabled. You need to disable SE Linux:

# Edit file "/etc/selinux/config"

# Change "SELINUX=enforcing" to "SELINUX=disabled"

# Save the file

# Restart your computer

Once SELinux is disabled, the configuration will complete on its own. 

You may need to [[Appion:reconfigure the database]] if the Tools web page is not displayed.

!SELinuxInstall.png! 

 

h2. A database was previously configured

If you see the errors shown in the screen below, you may have previously configured a database with mysql. You will need to re-install CentOS and run the installation script again.

!Screenshot.png!

h2. The Redux image server is not running

If you don't see micrograph images in the online image viewer, and instead see the word "empty" as shown in the screen below, you may need to start the Redux image server. The command is:

<pre>

/sbin/service reduxd start

</pre>

!reduxNotRunning.jpg!