Software Packages and Versions

The base Debian 10 OS is installed from an ISO disk. 

Linux  4.16.0-8-amd64 #1 SMP Debian 4.16.98-1+deb9u2 (2020-01-26) x86_64 GNU/Linux

Current version on Silicon Mechanics is :

Linux  4.16.0-8-amd64 #1 SMP Debian 4.16.98-1+deb9u2 (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 /sysadmin/install_scripts/debian10-init

Details for system administrators are here : Debian 10 OS for IBIC Neuroimaging Applications

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 

IBICIT

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/debian10-init/

Mount and run as root the following 4 scripts from /install_scripts/debian10-init/ 

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:631for workstation in IBIC Lab area.

reboot the computer to allow user authentication and authorization on the system to take effect.

2Ainstall_productivity

./productivity/install_latex  – 2.6-1.40.19

# latex needed for ess in R

./productivity/install_R – 3.6

./productivity/install_anaconda3  – anaconda3/python 3.7

# python install should come after R

./productivity/install_gnuplot – 5.2.6

./productivity/install_ppss – 2.97

./productivity/install_cmake – 3.13

./productivity/install_chrome – 80.0

./productivity/install_sublime – 3211

./productivity/install_virtualbox – 6.0

./productivity/install_octave – 4.4

./productivity/install_mrtrix -- 0.2.13

./productivity/install_mrtrix3 – 3.0

./productivity/install_imagemagick – 6.9.10

./productivity/install_gawk – 4.2.1

./productivity/install_eog

./productivity/install_nomachine – Desktop only, 6.3

./productivity/install_docker_repo – 19.03

./productivity/install_singularity – 2.5.2

./productivity/install_FastX  – 2.4 on servers only

./productivity/install_duplicity  – 0.8.11 on servers only, lolo backup utility

### matlab

./matlab/install_MCR81 – MATLAB runtime compiler v81

./matlab/install_MCR90 – MATLAB runtime compiler v90

./matlab/install_MCR901 – MATLAB runtime compiler v901

./matlab/install_MCR93 – MATLAB runtime compiler v93

./matlab/install_MATLAB – R2019a

## SGE

./SGE/install_sge62u5 – servers only

### NOTE that the SERVER must be rebooted before this script is run, for Kerberos/LDAP "sgeadmin" user to be present.

./productivity/install_python_packages:

pip install pyxnat==1.2.1

pip install nibabel==3.0.2

pip install nipy==0.4.2

pip install pydicom==1.4.2      

pip install nitime==0.8.1

pip install dipy==1.1.1

pip install mne==0.19.2

pip install PsychoPy==2020.1.2

pip install reportlab==3.5.42

#pip install rpy2==3.2.7 #install after R

pip install dcm2bids==2.1.4

pip install cfncluster==1.6.1

pip install paramiko==2.7.1

2Binstall_neurosoftware

./neurosoftware/install_afni – 20.0.18

./neurosoftware/install_afq – 1.2

./neurosoftware/install_ants – 1.9.1 and 2.3.2(default)

./neurosoftware/install_artfind – 2011

./neurosoftware/install_c3d – 1.0

./neurosoftware/install_camino – 3/13/16

./neurosoftware/install_connectomewb – 1.4.2

./neurosoftware/install_dcmtk – 3.6

./neurosoftware/install_dicom3tools – 2012

./neurosoftware/install_dtiprep – 1.2.8

./neurosoftware/install_fmripower – 1.0

# freesurfer is too big for USB key

./neurosoftware/install_freesurfer – 5.3

./neurosoftware/install_freesurfer6 -- 6.3

./neurosoftware/install_fsl-5.0.9

./neurosoftware/install_fsl-6.0

./neurosoftware/install_MRIConvert – 

./neurosoftware/install_mricron – 1.0.2

./neurosoftware/install_pipestat – 

./neurosoftware/install_qatools – 1.1

./neurosoftware/install_robex – 1.2

./neurosoftware/install_slicer – 4.5.0

./neurosoftware/install_spm8

./neurosoftware/install_spm12

# packages needs to be installed after matlab and spm

./neurosoftware/install_vbm  – 8r445

./neurosoftware/install_r2agui – 2.7