Appion

h1. Download additional Software (Fedora Specific)

h2. Install the additional package repositories 

Unlike RHEL/CentOS, Fedora comes with an Extras repository by default that contains all of the open source software needed by Appion/Leginon.

That said, there are several additional Fedora repositories that you can install. These repositories provide additional packages that are not allowed in the default Fedora package list, such as patented software (MP3 and Movie players), closed source applications (Nvidia video driver, Flash plugin, Adobe acrobat reader). But some repositories install packages over other packages, which can cause problems and conflicts (ATrpms is especially bad at this), so avoid these repositories. So, we recommend only installing RPM Fusion.

h3. RPM Fusion (optional)

* http://rpmfusion.org/

* good for mp3 and other patent limited software

Download repository rpms and install

<pre>

sudo rpm -Uvh http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-stable.noarch.rpm

sudo rpm -Uvh http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-stable.noarch.rpm

</pre>

h2. Update current packages 

.Update the updater to make life easier

<pre>

sudo yum -y update yum

</pre>

h3. Update all packages

<pre>

sudo yum -y update

</pre>

*NOTE*

Sometimes I have problems with 32bit packages, so uninstall of them:

<pre>

sudo yum remove `rpm -qa --qf "%{NAME}.%{ARCH}\n" | grep i.86`

</pre>

*NOTE*

Download was over 129 MB (in July 2009) and 333 MB (in May 2010). If you have a slow internet connection you can setup presto/deltarpms, see "this email":http://www.linux-archive.org/centos-development/222706-presto-deltarpm.html and "this email":http://www.centos.org/modules/newbb/viewtopic.php?topic_id=8349 for more information

You can also remove large packages like openoffice, java, and gimp to save space, if you are just making a server

<pre>

sudo yum remove openoffice* gimp* java*

</pre>

You will want to restart your computer when this completes.

h3. Install Complete list of additional packages:

General instructions for installation and configuration of some of these packages (such as mysql) are found later in this manual. It may be faster to install them now as a group rather than individually, but it is not necessary.

* *python tools*: python-tools python-devel

* *general applications*: subversion ImageMagick grace gnuplot python-matplotlib pstopnm (netpbm-progs)

* *Tilt Picker*: wxPython numpy scipy python-imaging

* *FindEM*: gcc-gfortran compat-gcc-34-g77

* *Ace 2*: gcc-objc fftw3-devel gsl-devel

* *Sinedon*: mysql mysql-server MySQL-python

* *Myamiweb*: httpd php php-mysql phpMyAdmin

* *Xmipp MPI*: gcc-c++ openmpi-devel libtiff-devel

* *MRC tools*: php-devel gd-devel re2c fftw2-devel php-gd

* *UCSF Chimera imaging*: xorg-x11-server-Xvfb

If you are using an RPM based system (e.g., SuSE, Mandriva, CentOS, or Fedora) "this website":http://rpm.pbone.net/ is good for determining the exact package name that you need. For CentOS 5, just type:

<pre>

sudo yum -y install \

python-tools python-devel python-matplotlib \

subversion ImageMagick grace gnuplot \

wxPython numpy scipy python-imaging \

gcc-gfortran compat-gcc-34-g77 \

gcc-objc fftw3-devel gsl-devel \

mysql mysql-server MySQL-python \

httpd php php-mysql phpMyAdmin  \

gcc-c++ openmpi-devel libtiff-devel \

php-devel gd-devel re2c fftw2-devel php-gd \

xorg-x11-server-Xvfb netpbm-progs

</pre>

If you have an nVidia video card and setup RPM fusion, install the nVidia binary, will speed things up especially for UCSF Chimera. This command works on Fedora

<pre>

sudo yum -y install nvidia-x11-drv

</pre>

for CentOS you will have to download and install the nvidia driver from the "nvidia website":http://www.nvidia.com

h4. Clean up packages to save drive space

<pre>

sudo yum clean all

</pre>

h4. Re-index the hard drive, this will come in handy later

<pre>

sudo updatedb

</pre>

h4. Enable web and database servers on reboot

<pre>

sudo /sbin/chkconfig httpd on

sudo /sbin/chkconfig mysqld on

</pre>

You can further configure this with the GUI and turn off unnecessary items

<pre>

system-config-services

</pre>

h4. Reboot the computer

<pre>

sudo reboot

</pre>

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[[Instructions for installing Fedora on your computer|< Instructions for installing Fedora on your computer]] | [[Complete Installation|Complete Installation ^]]

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