Software Packages and Versions
The base Debian 8 OS is installed from an ISO disk. Servers from SiliconMechanics come with the OS installed
Linux 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1+deb8u2 (2016-10-19) x86_64 GNU/Linux
Current version from Silicon Mechanics is :
Linux 3.16.0-4-amd64 #1 SMP Debian 3.16.43-2+deb8u5 (2017-09-19) x86_64 GNU/Linux
Installer scripts are checked into the IBIC GitHub repository https://github.com/IBIC, and reside locally on the NAS in /install_scripts/debian8
Details for system administrators are here : Debian 8 OS for IBIC Neuroimaging Applications
There are no filesystems mounted yet; These four install scripts are on a USBkey : Debian8installer.
A) for servers with RAID arrays, this script will mount at /export/<servername>
USBconfigure_network
hostname, IP address, ethernet port 0 (default), file system mountpoints, fstab
exports RAID
B) for most workstations, without RAID array, and/or if the RAID is not exported.
noRAID_USBconfigure_network
hostname, IP address, ethernet port 0 (default), file system mountpoints, fstab
kwUser, karlUser
shared admin and admin account setup, interactive credential inputs.
Once the USBkey scripts are run, reboot the machine and verify hostname, ip, ethernet connectivity, and mounts
NEXT - from /install_script/debian8
Mount and run as root the following 4 scripts from /install_scripts/debian8
1.0install
gpp keys, apt repositories, sshd configuration, X2go server and client, xfce4, sudo, usbmount, ntpdate, /etc/bash.bashrc, haveged, gedit, gnome-disk-utility, lsb_release, cups
./install_Kerberos
./Install_LDAP
./install_automounter
./install_email
Following this install, you should install the IBIC printer driver /install_scripts/debian8/sources/Ricoh-PM_C4504-pxlcolor-Ricoh.ppd, using the CUPS interface localhost:631
2Ainstall
./install_dicom3tools - 20110207
./install_freesurfer - stable 5.3
./install_freesurfer6 - stable 6.0
./install_fsl - 5.0.9
./install_afni_test17
./install_mricron- 4 AUGUST 2014
./install_spm12
./install_spm8
./install_dcmtk - 3.6
./install_pipestat - legacy 32bit binaries ca. 1990
./install_camino 3/13/16
./install_fmripower 1.0
./install_ants - 1.9.1 and 2.1.0 rc3
./install_artfind - April 28, 2011
./install_afq - 1.2
./install_mrtrix - 0.2.12
./install_dtiprep - 1.2.4
./install_cmake - 3.0.2
./install_qatools - 1.1
./install_robex - 1.2
./install_r2agui - 2.7
./install_connectomewb - 1.1.1
A) for workstations and non-SuperMicro servers
2Binstall
./install_vbm - 8r445
./reinstall_R
./install_gkrellm - 2.3.6-RC1
./install_gnuplot - 4.6.6-2
./install_slicer - 4.5.0
./install_c3d
./install_scrot - 0.8-13
./install_chrome - current stable
./install_python - Anaconda 4.3.4
with:
./install_pyxnat
./install_nibabel
./install_build-essential
./install_nipype
./install_nipy
./install_swig
./install_pymvpa
./install_pydicom
./install_nitime
./install_dipy
./install_mne
./install_psychopy
./install_reportlab
./install_rpy2
./install_npfile
./install_ppss - 2.97
./install_gawk - 4.1.1
./install_mcverter
./install_latex - 2.6-1.40.15
./install_sublime - 3103
./install_261optimusep
./install_MATLAB - 2016a
./install_MCR901 - MATLAB Runtime v901
./install_MCR90 - MATLAB Runtime v90
./install_MCR81 - MATLAB Compiler Runtime v81
./install_network_MATLAB_license
./install_imagemagick - unspecified, 6.8.9-9
./install_MRIConvert - 2.0.8 build 416
./install_StarCluster - awscli - 1.10.60, starcluster - 0.95.6
./install_cfncluster - 1.3.1
./install_subversion_etc - subversion 1.8.10, tree 1.7.0, debconf-utils 1.5.56, xclip 0.12, recode 3.6
./install_docker - 1.12.1
OPTIONAL, for neuron-class servers only
B) for workstations and non-SuperMicro servers
2BinstallSERVER
Full install script adds :
./install_duplicity
./install_sge62u5 ### NOTE that the SERVER must be rebooted before this script is run, for Kerberos/LDAP "sgeadmin" user to be present
./install_FastX
2Cinstall
./install_Rniftilib
./install_xtermStyle
./install_datamerge
./install_eog
./install_virtualbox-5.0
./install_octave
./install_ntp
./install_monit