Uppsala Multidisciplinary Center for Advanced Computational Science

How to handle the INBOX folder

WARNING: The INBOX folder is not backed up. Make sure to move your files elsewhere as soon as possible.

(This guide assumes that you know how to connect and log in to Uppmax via SSH. If you don't, read the login guide)

Data delivered from the genomic platforms will be placed in your project's INBOX folder. It is important to keep your inbox empty, since EVERYONE using Uppmax have write permissions in the inbox folder. That means that anyone can edit or delete your files. Fortunately, most users at Uppmax do not indulge in this kind of behavior, but it is always better to be safe than sorry. The fact that the INBOX folder is not backed up, also means that genomics platforms deliveries that can not be repeated should not be left within INBOX, but instead moved to a backuped area.

So, to move your files to a safe location, follow these steps:

The project that will be used in this example will be called 'b2011999'. Just substitute this project name with the one for your project.

1. Connect to Uppmax via SSH. Read the login guide if you want help with that.
2. Change directory to your project folder: (cd )

cd /proj/b2011999

3. Create a new directory for your files: (mkdir )

Here you might want to consider if you should use the 'private' folder or not. There is a folder in your project folder named 'private' (type ls while in your project folder to view files and folders). Files placed within this folder will ONLY be visible to project members. This is a good option if you want to keep others from accessing your data. It is not a good option if you would like to collaborate with other people than your project members.

To create a directory named myFolderName (can be substituted with any name you would like) INSIDE the private folder (private folder, accessible only to project members):

mkdir private/myFolderName

To create a directory named myProjectName (can be substituted with any name you would like) OUTSIDE the private folder (open folder, accessible to non-project members):

mkdir myFolderName

4. Copy your files to your newly created folder (could take a while, depending on the file sizes. Big file = long time): (cp )

WARNING: This will copy ALL files in the INBOX folder. If you have multiple files belonging to different projects in your inbox, please copy them separately.

To a private folder:

cp -r INBOX/* private/myFolderName/

To an open folder:

cp -r INBOX/* myFolderName/

5. Remove the files in the inbox folder after they have been successfully copied to a new folder (step 4): (rm )

WARNING: This will remove ALL files from the INBOX folder! If you have files in the INBOX that have not been copied to the correct location yet, please repeat step 3-4 for these files before completing step 5!

rm -r INBOX/*