How to upload your own files to IVM via /finngen/green

Step 1:

When you get access to FinnGen Sandbox, you are told in which bucket your cloud storage is (“fg-production-sandbox-6_greenuploads” in the following example) or you can also lookup this information from the file "buckets.txt" on the desktop of the IVM. The location of “buckets.txt” file in the IVM desktop is demonstrated here). This is the place where you can upload files to “/finngen/green” directory.

Step 2:

Select “UPLOAD FILES” which opens a file selection dialog on your own computer. Suppose you’d like to upload the file “An_example.txt” to the green library. It would show up as in the following image.

URLs to greenuploads and greendownloads buckets are:

• https://console.cloud.google.com/storage/browser/fg-production-sandbox-N_greenuploads

• https://console.cloud.google.com/storage/browser/fg-production-sandbox-N_greendownloads

Where N is the number of your institution Sandbox.

Note! After a security update in July 2024, you can't anymore see the files you have uploaded to the greenuploads bucket in the GCP console. In other words, the file listing is invisible to you and instead you see a warning how you can't see the files etc. However, you can still upload the files and they will proceed to virus scanning (step 3) and appear in green bucket if the virus scan was ok. The same applies, if you had personal folders in the greenuploads bucket. The folders are not listed but you can still "go" to the existing folders or create new ones. In other words, if you have a folder called my_uploads, you can simply navigate there with URL: https://console.cloud.google.com/storage/browser/fg-production-sandbox-N_greenuploads/my_uploads

Step 3:

Now your file will go through an automatic virus scan. A virus scan will take from 5 to 20 min. If the virus scan is clear the file will be uploaded to the green folder in your Sandbox IVM. If the file doesn't pass the virus scan it will be contained. If your file does not appear in the green bucket after reasonable delay contact [e-mail]. Virus scan is not able to handle large files (5 GB or more) these files are not moved to /finngen/green. If you need to import large files to Sandbox they should be subsetted into multiple files. This can be done with zip tools in many operation systems and compiled into one file in Sandbox.

Step 4:

After upload you can navigate to your file either by using the graphical user interface (“File System/finngen/green”) or the command line (“/finngen/green”).

More guidance about How to load R packages to your Sandbox IVM, Python package, and GNU Debian package.