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NeuroDesk / neurocontainers

The containers can be used in combination with our transparent singularity or neurocommand tool, that wrap the executables inside a container to make them easily available for pipelines
https://www.neurodesk.org
MIT License
19 stars 52 forks source link

software containers to be installed #8

Closed stebo85 closed 4 years ago

stebo85 commented 4 years ago

https://docs.google.com/document/d/1KWznhJH7GzjmB1TK5veAH5FejcsjUs70pMmQloHph0g/edit

NeuroDesk/VNM project

Software to add to "library" of containers / "master" container

Bold - Software already in the library (available through https://github.com/ReproNim/neurodocker)

General

General neuroimaging

General MRI

Structural MRI

Functional MRI

Diffusion MRI

EEG/MEG BrainStorm (MATLAB software) Fieldtrip (MATLAB software)

EEG

MEG MNELab

Connectomics

Multivariate/MVPA CosmoMVPA (Matlab toolbox) RSA Toolbox (http://www.mrc-cbu.cam.ac.uk/methods-and-resources/toolboxes/)

MartinGrignard commented 4 years ago

I started adding softwares using the small script I added to the image. For now I simply add .desktop files, no submenus or anything but we might want to add sub menus for each software to group versions.

(see branch add-softwares)

Now I see that @aswinnarayanan added some information on how to add submenus so I'll take a look to that later.

MartinGrignard commented 4 years ago

I added instructions on how to add tools in the wiki here. If something does not fit with the idea you had, it can still be modified, but for now it works quiet well :)

stebo85 commented 4 years ago

Wow, that is awesome!!!! Thank you so much. Have you already added applications using this method in a branch? The master branch doesn't seem to have anything yet :?

On Fri, 19 Jun 2020 at 04:49, Martin Grignard notifications@github.com wrote:

I added instructions on how to add tools in the wiki here https://github.com/NeuroDesk/vnm/wiki/Add-a-tool-to-VNM. If something does not fit with the idea you had, it can still be modified, but for now it works quiet well :)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/NeuroDesk/vnm/issues/6#issuecomment-646243809, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA6V2WYZKPZHIYRVM5IEWZTRXJOVBANCNFSM4OA7ND6A .

MartinGrignard commented 4 years ago

I've tried with ITK snap and two versions of FreeSurfer in the branch here and it worked like a charm :) feel free to test it, we might end up editing the fetch_and_run.sh file in order to make it more versatile (set the repository to pull from as it is available in transparent-singularity, show a progress bar during download, etc) but for now its is enough to achieve what we want :)

[EDIT] One thing which would be interesting is, as I tried to do for FreeSurfer, for each tool:

We also discussed with @kaczmarj about the fact that some tools provide way too much binaries (way more than the majority of users ever use) so we could add a way to make small installs. This would really reduce the size of the images to fetch. For Freesurfer, downloading 2.4GB took way too long from here in Belgium. (I've starting talking with my supervisor about creating a mirror for the image repository here). This means that we have to list, for each tool, the main binaries (eg recon-all for FreeSurfer).

stebo85 commented 4 years ago

I created separate issues for the software that we would like to have in the respective repos