Download additional Software (CentOS Specific)¶
Install the additional package repositories¶
There are several additional CentOS repositories that you can install. These repositories provide additional packages, such as patented software (MP3 players), closed source applications (Flash plugin, Adobe Acrobat Reader) and lesser used packages (python numpy, Gnu Scientific Library). But some repositories install packages over other packages, which can cause problems and conflicts (ATrpms is bad at this). So we recommend only installing EPEL and RPM Fusion. Read more here:
CentOS Additional Repositories
Particularly, pay attention to the note about protecting yourself from unintended updates from 3rd party packages. The following yum plugin may help you:
yum-priorities plugin
Extra Packages for Enterprise Linux (EPEL)¶
- http://fedoraproject.org/wiki/EPEL
- contains a wealth of packages required for appion
Download repository rpm and install
wget 'http://mirrors.cat.pdx.edu/epel/6/i386/epel-release-6-8.noarch.rpm' sudo yum --nogpgcheck localinstall epel-release-6-8.noarch.rpm
Note that release version (6-8) is the current release at the time of this writing. Please visit http://fedoraproject.org/wiki/EPEL/FAQ#How_can_I_install_the_packages_from_the_EPEL_software_repository.3F for more up-to-date information on how to install the packages from the EPEL software repository.
RPM Fusion (optional)¶
- http://rpmfusion.org/
- good for mp3 and other patent limited software
Download repository rpms and install
sudo rpm -Uhv http://download1.rpmfusion.org/free/el/updates/testing/5/`uname -i`/rpmfusion-free-release-5-0.1.noarch.rpm sudo rpm -Uvh http://download1.rpmfusion.org/nonfree/el/updates/testing/5/`uname -i`/rpmfusion-nonfree-release-5-0.1.noarch.rpm
Update current packages¶
Update the updater to make life easier
sudo yum -y update yum*
Update all packages¶
sudo yum -y update
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 and this email for more information
NOTE
Sometimes I have problems with 32bit packages, so uninstall of them:
rpm -qa --qf "%{NAME}.%{ARCH}\n" | grep i.86 | wc -l sudo yum remove `rpm -qa --qf "%{NAME}.%{ARCH}\n" | grep i.86`
NOTE
You can also remove large packages like openoffice, java, and gimp to save space, if you are just making a server
sudo yum remove openoffice* gimp* java*
You will want to restart your computer when this completes.
sudo reboot
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
- UCSF Chimera imaging: xorg-x11-server-Xvfb
- PHP-SSH2: libssh2-devel
If you are using an RPM based system (e.g., SuSE, Mandriva, CentOS, or Fedora) this website is good for determining the exact package name that you need. For CentOS 5, just type:
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 fftw3-devel php-gd \ xorg-x11-server-Xvfb netpbm-progs \ libssh2-devel
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
sudo yum -y install nvidia-x11-drv
for CentOS you will have to download and install the nvidia driver from the nvidia website
Clean up packages to save drive space¶
sudo yum clean all
Re-index the hard drive, this will come in handy later¶
sudo updatedb
Enable web and database servers on reboot¶
sudo /sbin/chkconfig httpd on sudo /sbin/chkconfig mysqld on
You can further configure this with the GUI and turn off unnecessary items
system-config-services
Reboot the computer¶
sudo reboot
< Instructions for installing CentOS on your computer | Database Server Installation >
Updated by Anchi Cheng about 8 years ago · 47 revisions