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CentOS Imaging installation transcript

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christinerogers edited this page Jul 28, 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 may no longer need to be run manually for CentOS.

This transcript is offered as a helpful guide but by no means an exhaustive roadmap to installing every dependency for the MINC and DICOM toolkit.

  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

CAVEAT: no longer relevant for Loris-MRI 16.* -- see Loris-MRI Readme for your Release code instead

[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 toolkit:
[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. Ensure the .bashrc files contains the following line, to source the MINC toolkit:
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

If CharLS is not already installed and is not easily findable, try:

sudo yum --enablerepo=epel install CharLS
  1. Cpan to install needed Perl libraries
[lorisadmin@PROJ ~]$ sudo cpan
cpan1> install Math::Round
cpan2> install Getopt::Tabular
cpan3> install Time::JulianDay

Note: the following command failed - see step 9 below

cpan4> install Path::Class

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

If this doesn't work for your system, try:

sudo yum --enablerepo=epel install perl-Path-Class
  1. Source the .bashrc file
[lorisadmin@PROJ mri]$ source ~/.bashrc
  1. 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) Note modifications to php.ini recommended in the Imaging Uploader Module Readme https://github.com/aces/Loris/blob/master/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.* 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:

git fetch origin
git pull origin master
git submodule update (to update the dicom-archive submodule)

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

<!-- MINC TOOLS PATH -->
<MINCToolsPath>/opt/minc/</MINCToolsPath>

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