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Hello Chiara,

It reads like Code Ocean wants to be a solution for someone to host all their research files for published articles, scripts, applications and binaries to run - in 1 place.  But it’s not clear to me applications/scripts/binaries can be run from there in real-time.  It looks more like another form of source control, e.g., GitHub, to enable sharing and managing of files (including disaster recovery). 

The text at the bottom of this page, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://codeocean.com/product/, indicates they use Amazon AWS servers.  So maybe a code capsule would connect with and run software via an AWS server image with the needed software installed.  That server would in turn need to run a flavor of linux that would allow installing one of the freesurfer distribution packages from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard..edu/fswiki/rel7downloads.

For scientific clusters, you usually file a ticket to request installation of a software package not already available to run on the cluster.  I would ask Code Ocean tech support how a code capsule currently runs python scripts and/or linux binaries in real-time from a users account.  If that already works to run python scripts or some programs installed on linux servers, then you could ask tech support how 3rd party software packages (like freesurfer) could be managed and installed to run from a users account.

- R.

On Feb 24, 2023, at 03:50, Chiara Marzi - UniFI <chiara.marzi@unifi.it> wrote:

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Dear Freesurfer,

I am trying to use some FreeSurfer tools inside a Code Ocean capsule (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://codeocean.com/), a cloud-based computational reproducibility platform that provides researchers and developers an easy way to share, discover, and run code published in academic journals and conferences. 

Specifically, I set up my capsule environment including a Python package (freely available at Github: XXX) that requires FreeSurfer for full functionality. Is it possible to install FreeSurfer on such a platform? Do you have any suggestions?

Thanks!

Have a nice day,
Chiara
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