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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

 


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