Skip to content

CentOS Imaging installation transcript

Jump to bottom
christinerogers edited this page Jul 26, 2016 · 21 revisions

CAVEAT: THIS TRANSCRIPT is a record of a successful Loris-MRI 15.10 installation on CentOS.
For Loris-MRI 16.0, several of these steps have been automated/included in the install process and need no longer be run manually.

  1. Checking if some needed dependencies (needed by the minc toolkit and/or dicom toolkit) are installed:

a) [lorisadmin@PROJ mri]$ yum list installed 'libstdc*' b) [lorisadmin@PROJ mri]$ yum list installed 'glibc' c) [lorisadmin@PROJ ~]$ yum list installed 'gcc*' d) [lorisadmin@PROJ mri]$ yum list installed 'perl*'

  1. Creating directories:

[lorisadmin@PROJ data]$ sudo mkdir /data/PROJ/ [lorisadmin@PROJ data]$ cd [lorisadmin@PROJ ~]$ [lorisadmin@PROJ ~]$ sudo chown -R lorisadmin:lorisadmin /data/PROJ [lorisadmin@PROJ ~]$ mkdir /data/PROJ/bin [lorisadmin@PROJ ~]$ mkdir /data/PROJ/bin/mri [lorisadmin@PROJ ~]$ mkdir /data/PROJ/data [lorisadmin@PROJ ~]$ mkdir /data/PROJ/tarchive [lorisadmin@PROJ ~]$ mkdir /data/PROJ/trashbin [lorisadmin@PROJ ~]$ mkdir /data/PROJ/assembly [lorisadmin@PROJ ~]$ mkdir /data/PROJ/jiv [lorisadmin@PROJ ~]$ mkdir /data/PROJ/pic [lorisadmin@PROJ ~]$ mkdir /data/PROJ/logs

[lorisadmin@PROJ mri]$ sudo mkdir /data/PROJ/data/batch_output [lorisadmin@PROJ mri]$ sudo mkdir /data/PROJ/bin/mri/dicom-archive/.loris_mri [lorisadmin@PROJ dicom-archive]$ sudo chown -R lorisadmin:lorisadmin .loris_mri/

[lorisadmin@PROJ ~]$ sudo mkdir /data/incoming [lorisadmin@PROJ ~]$ sudo chown -R lorisadmin:lorisadmin /data/incoming

  1. Cloning LORIS-MRI repo

[lorisadmin@PROJ ~]$ cd /data/PROJ/bin

no longer relevant for Loris-MRI 16.* -- see Loris-MRI Readme

[lorisadmin@PROJ bin]$ git clone https://github.com/aces/Loris-MRI.git mri [lorisadmin@PROJ mri]$ git submodule init [lorisadmin@PROJ mri]$ git submodule sync [lorisadmin@PROJ mri]$ git submodule update

  1. Installing ImageMagick needed by the minc toolkit:

[lorisadmin@PROJ mri]$ sudo yum install ImageMagick [sudo] password for lorisadmin:

  1. Installing minc tools:

[lorisadmin@PROJ mri]$ cd [lorisadmin@PROJ ~]$ wget http://packages.bic.mni.mcgill.ca/minc-toolkit/RPM/minc-toolkit-1.0.08-20160205-CentOS_6.7-x86_64.rpm [lorisadmin@PROJ opt]$ sudo rpm -Uvh ~/minc-toolkit-1.0.08-20160205-CentOS_6.7-x86_64.rpm [sudo] password for lorisadmin:

  1. Edit the .bashrc file to source the minc tools

[lorisadmin@PROJ minc]$ sudo nano ~/.bashrc

Ensure the .bashrc files contains the following line: source /opt/minc/minc-toolkit-config.sh

  1. Install DICOM toolkit (CharLS was needed first as a dependency)

[lorisadmin@PROJ minc]$ cd [lorisadmin@PROJ ~]$ wget http://tissuestack.org/downloads/CentOS/dcmtk-3.6.0-0.el6.x86_64.rpm [lorisadmin@PROJ ~]$ sudo yum -y install CharLS [sudo] password for lorisadmin: [lorisadmin@PROJ ~]$ sudo rpm -i -v dcmtk-3.6.0-0.el6.x86_64.rpm

  1. Cpan to install needed Perl libraries

[lorisadmin@PROJ ~]$ sudo cpan cpan1> install Math::Round cpan2> install Getopt::Tabular cpan3> install Time::JulianDay

cpan4> install Path::Class

THIS COMMAND FAILED

cpan5> install Archive::Extract cpan6> install Archive::Zip cpan7> quit

  1. Install the failed Path library as follows: [lorisadmin@PROJ ~]$ sudo yum install perl-Path-Class

  2. [lorisadmin@PROJ mri]$ source ~/.bashrc

  3. Use the imaging_install.sh script to do the remaining steps (lines were commented out from the installation script as they were done manually in the steps above; the attached .txt file has the detailed lines that were commented out)

CAVEAT again: THIS TRANSCRIPT refers to the 15.10 imaging_install.sh script. SOME STEPS manually executed in this transcript are no longer necessary for Loris 16.*

[lorisadmin@PROJ mri]$ bash ./imaging_install.sh

MINC Toolkit appears to be installed. What is the database name? PROJ What is the database host? ###.###.###.# What is the MySQL user? lorisdbadmin What is the MySQL password? ############ What is the Linux user which the installation will be based on? lorisadmin What is the project name? PROJ What is your email address? ###.###@gmail.com What prod file name would you like to use? default: prod Enter the list of Site names (space separated) Modifying environment script

Creating MRI config file config file is located at /data/PROJ/bin/mri/dicom-archive/.loris_mri/prod

end of imaging_install.sh output

Further notes / modifications:

b) Adding to the nginx conf tnl.conf (limits of 2000M), otherwise, Imaging Uploader might issue a "413 Request Entity Too Large" error when uploading a file

c) Setting some php.ini values for the imaging uploader to work as per the recommendations on the Imaging Uploader Loris page (https://github.com/aces/Loris/blob/16.04-dev/modules/imaging_uploader/README.md)

d) installation of DBD::mysql required for the imaging pipeline scripts.

[lorisadmin@PROJ ~]$ sudo cpan [sudo] password for lorisadmin: Terminal does not support AddHistory.

cpan shell -- CPAN exploration and modules installation (v1.9402) Enter 'h' for help.

cpan1> install DBD::mysql

BUT THIS FAILED... the last few lines of the execution gives: make: *** [dbdimp.o] Error 1 CAPTTOFU/DBD-mysql-4.033.tar.gz /usr/bin/make -- NOT OK Warning (usually harmless): 'YAML' not installed, will not store persistent state Running make test Can't test without successful make Running make install Make had returned bad status, install seems impossible Failed during this command: CAPTTOFU/DBD-mysql-4.033.tar.gz : make NO

So I re-installed using: [lorisadmin@PROJ ~]$ sudo yum install "perl(DBD::mysql)" [sudo] password for lorisadmin:

THIS SEEMS TO WORK, with the last few messages:

Installed: perl-DBD-MySQL.x86_64 0:4.013-3.el6

Complete!

e) the following steps were required in Loris 15.10, but are now covered in the 16.0 imaging install process:

In /data/ directory, enable apache user to upload using the imaging uploader, but we also want lorisadmin to be able to process the data:

  1. [lorisadmin@PROJ data]$ sudo chown lorisadmin:apache incoming/
  2. [lorisadmin@PROJ data]$ sudo chmod 770 incoming/
  3. [lorisadmin@PROJ data]$ sudo chmod g+s incoming/ Our install script now makes lorisadmin part of apache group (they have to be part of the same group to be able to read/write into same directories for processing and to be able to load brainbrowser in the front-end): sudo usermod -a -G apache lorisadmin

/data/PROJ/bin/mri/environment file updated to reflect latest release (namely source the minc toolkit and umask 0002) updated the Loris-MRI code base to 16.0.0 release as follows: (with Zia) git fetch origin (with Zia) git pull origin master git submodule update (to update the dicom-archive submodule)

in /var/www/PROJ/project/config.xml: I added:

/opt/minc/

Home | About | Community | Setup | Technical

Clone this wiki locally