Instructions for LEGA users (SDA implementation)

Prerequisites

You must be able to use a shell terminal. The instructions are directioned towards Linux environments, but other environments can do the same using similar tools.

Install sda-cli

• Download sda-cli, the tool used to upload data into FEGA. There are different releases available here. If you are using a terminal, you can run the following command to download the Linux version:

wget https://github.com/NBISweden/sda-cli/releases/download/v0.3.0/sda-cli_.0.3.0_Linux_x86_64.tar.gz

• Extract the tool (substitute the filename, if needed):

tar -xzvf sda-cli_.0.3.0_Linux_x86_64.tar.gz

• When doing submissions, you will need to call the sda-cli file from the terminal (e.g., using ./sda-cli).
• (Optional) Add sda-cli to system-wide binaries (you need root access!):

sudo cp sda-cli /usr/bin

Getting the server's public key

• Download the Portuguese LEGA's public key from https://inbox.ega.biodata.pt/c4gh.pub.pem . You can download it using a web browser or using wget https://inbox.ega.biodata.pt/c4gh.pub.pem . The downloaded file should look like this:

-----BEGIN CRYPT4GH PUBLIC KEY-----
B2gV8b0FoVLDz0x156JBpLXdB069w4UTtWYeQf9Yzz4=
-----END CRYPT4GH PUBLIC KEY-----

Configuration file

• Create a file named s3cmd.conf using the following template and replace the values of access_key and secret_key with your EGA username:

[default]
encoding = UTF-8
guess_mime_type = True
use_https = True
host_base = https://inbox.ega.biodata.pt
host_bucket = https://inbox.ega.biodata.pt
human_readable_sizes = True
multipart_chunk_size_mb = 50
socket_timeout = 30
access_key = <EGA USERNAME>
secret_key = <EGA USERNAME>
access_token = <ACCESS TOKEN>

• You can leave the access token as is for now, you will get it once you login. The access token is valid for 7 days, so you will need to replace it every now and then.

Uploading a file

Configuring credentials

• Go to https://login.ega.biodata.pt and login using EGA. If you don't have EGA credentials, visit this URL.
• Copy the access token (the long text starting with "eyJ") and put it in the s3cmd.conf file. Note: Try using triple-click on the text to select everything.
• You may also click on "Download credentials to upload to the inbox" to get a ready-made configuration file when logging in, but please delete the lines setting check_ssl_hostname and check_ssl_certificate to False.

Uploading

• After installing sda-cli, having the server's public key, and configuring a s3cmd.conf file, you are ready to upload a file. Use the following command and check the result:

./sda-cli -config s3cmd.conf upload -encrypt-with-key c4gh.pub.pem <FILE TO UPLOAD>

• If an error is returned, check if the all the paths you are using are right and that the access token is still valid.
• To check if the upload was successful, run the following command to see what files are in your inbox:

./sda-cli -config s3cmd.conf list

• If the file you uploaded appears in the list, the file was successfully uploaded!