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FreeSurfer: Difference between revisions
→Installation in a shared folder
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==Installation in a shared folder== | ==Installation in a shared folder== | ||
It is possible to | |||
Using EasyBuild, it is possible to install the program in a shared location (like project) and make the code available for any other member of the group. The following will install freesurfer under the project <code>def-someuser</code> and the module under the user's directory <code>/home/$USER/.local/easybuild/modules/2017</code>. | |||
The instructions are: | |||
{{Commands: | |||
|newgrp def-someuser | |||
|installdir=/home/$USER/projects/def-someuser/$USER | |||
|moduledir=/home/$USER/.local/easybuild/modules/2017 | |||
|pathtosrc=/home/$USER/software | |||
|eb FreeSurfer-6.0.1-centos6_x86_64.eb --installpath-modules=${moduledir} --prefix=${installdir} --sourcepath=${pathtosrc} --disable-enforce-checksums | |||
}} | |||
To make the program accessible for all members of the group, two more steps are required: | |||
* You need to give all members of your group read and exec access to the installation directory </home/$USER/projects/def-someuser/$USER>. To see how to give them access to this directory, please visit the [[Sharing data/en|data sharing]] page. | |||
8. Each member of the group will need to install the module file in their own home directories. The module file is within the directory: | |||
<pre> | |||
/home/$USER/.local/easybuild/modules/2017 | |||
</pre> | |||
tar file "/home/mcorrito/software/modules.tar". You can send them this file and they should run the following: | |||
- upload the file "modules.tar" to their home directory | |||
- Then create a directory if not already created: | |||
mkdir -p /home/$USER/.local/easybuild | |||
- Move the file "modules.tar" to "/home/$USER/.local/easybuild" and unpack it: | |||
mv modules.tar /home/$USER/.local/easybuild/ | |||
cd /home/$USER/.local/easybuild/ | |||
tar -xvf modules.tar | |||
The above will set the module (only the module file that points to the installation directory under project) in their own directory. | |||
The module can be loaded from their own accounts using: | |||
module load stata/15 | |||
It is possible to install the ed files (with Easybuild) to the project space, but permissions have to be fixed. | |||
* Recursively set the proper group ID of the freesurfer directory | * Recursively set the proper group ID of the freesurfer directory | ||
* Move the data to the desired location in the project space | * Move the data to the desired location in the project space | ||
* Copy the module file to a shared location, and edit all paths in the module file. | * Copy the module file to a shared location, and edit all paths in the module file. | ||