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FreeSurfer: Difference between revisions
Adapted the path from 2017 to 2020 for StdEnv/2020
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(Adapted the path from 2017 to 2020 for StdEnv/2020) |
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==Installation in your /home directory with EasyBuild== <!--T:6--> | ==Installation in your /home directory with EasyBuild== <!--T:6--> | ||
The following procedure will install FreeSurfer 6.0.0 in <code>/home/$USER/.local/easybuild/software/ | The following procedure will install FreeSurfer 6.0.0 in <code>/home/$USER/.local/easybuild/software/2020/Core/freesurfer/6.0.0/</code>. The installation of FreeSurfer requires some memory and due to the restrictions of memory stack size on the login nodes on Compute Canada clusters, the installation may fail because of the memory. To overcome this issue, you may need to use an [[Running_jobs#Interactive_jobs|interactive job]] by asking for enough memory (8 GB or so) to install the code. | ||
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==Installation in a shared folder== <!--T:12--> | ==Installation in a shared folder== <!--T:12--> | ||
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 directory <code>/home/$USER/projects/def-someuser/$USER/software</code> and the module under the user's directory <code>/home/$USER/.local/easybuild/modules/ | Using EasyBuild, it is possible to install the program in a shared location (like /project) and make the code available for any other member of the group. The following will install FreeSurfer under the directory <code>/home/$USER/projects/def-someuser/$USER/software</code> and the module under the user's directory <code>/home/$USER/.local/easybuild/modules/2020/Core/freesurfer</code>. | ||
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newgrp def-someuser | newgrp def-someuser | ||
installdir=/home/$USER/projects/def-someuser/$USER | installdir=/home/$USER/projects/def-someuser/$USER | ||
moduledir=/home/$USER/.local/easybuild/modules/ | moduledir=/home/$USER/.local/easybuild/modules/2020 | ||
pathtosrc=/home/$USER/software | pathtosrc=/home/$USER/software | ||
eb FreeSurfer-6.0.1-centos6_x86_64.eb --installpath-modules=${moduledir} --prefix=${installdir} --sourcepath=${pathtosrc} | eb FreeSurfer-6.0.1-centos6_x86_64.eb --installpath-modules=${moduledir} --prefix=${installdir} --sourcepath=${pathtosrc} | ||
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* Each member of the group will need to put the module file in their own /home directories. The module file <code>6.0.1.lua</code> is located under the directory: | * Each member of the group will need to put the module file in their own /home directories. The module file <code>6.0.1.lua</code> is located under the directory: | ||
<pre> | <pre> | ||
/home/$USER/.local/easybuild/modules/ | /home/$USER/.local/easybuild/modules/2020/Core/freesurfer/</code> | ||
</pre> | </pre> | ||
<!--T:17--> | <!--T:17--> | ||
Each member of the group will need to create the directory <code>/home/$USER/.local/easybuild/modules/ | Each member of the group will need to create the directory <code>/home/$USER/.local/easybuild/modules/2020/Core/freesurfer</code> where they will put the file <code>6.0.1.lua</code>: | ||
</translate> | </translate> | ||
{{Commands | {{Commands | ||
|mkdir -p /home/$USER/.local/easybuild/modules/ | |mkdir -p /home/$USER/.local/easybuild/modules/2020/Core/freesurfer | ||
|cp 6.0.1.lua /home/$USER/.local/easybuild/modules/ | |cp 6.0.1.lua /home/$USER/.local/easybuild/modules/2020/Core/freesurfer/ | ||
}} | }} | ||
<translate> | <translate> | ||