diff --git a/README.md b/README.md index e510df7e..5dc8807f 100644 --- a/README.md +++ b/README.md @@ -49,9 +49,9 @@ wget https://raw.githubusercontent.com/NBISweden/EGA-SE-user-docs/main/crypt4gh_ wget https://raw.githubusercontent.com/NBISweden/EGA-SE-user-docs/main/crypt4gh_bp_key.pub ``` -### Encrypt file(s) +### Encrypt files -After downloading the public key file, you can encrypt your file(s) using the +After downloading the public key file, you can encrypt your files using the `sda-cli` executable obtained in the first step of this guide. To encrypt a specific file, use the following command: @@ -75,7 +75,7 @@ command like this: ./sda-cli encrypt -key -continue=true ``` -### Encrypt file(s) with multiple keys +### Encrypt files with multiple keys You can encrypt files using multiple public keys by specifying the `-key` flag multiple times. For example: @@ -136,9 +136,9 @@ ways, listed in order of priority: 2. From the `ACCESSTOKEN` environment variable. 3. In the configuration file. -### Upload file(s) +### Upload files -Once the configuration file has been downloaded, file(s) can be uploaded to the +Once the configuration file has been downloaded, files can be uploaded to the archive using the `sda-cli` executable. To upload a specific file, use the following command: @@ -163,7 +163,7 @@ separated by spaces, as shown below: - If the input contains unencrypted files, the process will exit early. To override this behavior, use the `-force-unencrypted` flag. -### Upload folder(s) +### Upload folders You can upload entire directories recursively, including all contained files and subfolders while preserving the local folder structure. This can be done using @@ -205,7 +205,7 @@ The `` argument can also include a folder path, such as to `folder1/folder2/`. **Note**: To include all the contents of a directory without the directory -*itself, you can use `/.`. For instance: +itself, you can append `/.` to ``. For instance: ```bash ./sda-cli -config upload -r /. -targetDir @@ -243,7 +243,7 @@ the folder recursively (including only the resulting `.c4gh` files) under - The command internally calls the [encrypt](#Encrypt) module when performing encrypt-on-upload, mirroring its behavior, including the creation of hash files. -- For encryption with [multiple public keys](#Encrypt-file(s)-with-multiple-keys), +- For encryption with [multiple public keys](#Encrypt-files-with-multiple-keys), concatenate all public keys into a single file and provide it using the `-encrypt-with-key` flag. - If the input includes already encrypted files, the process will exit without @@ -310,9 +310,9 @@ Depending on the setup of the SDA/BP services, files can be downloaded unencrypted or encrypted. If the service is configured for encrypted downloads, you can download files -encrypted on the server-side by providing a [public key file](#create-key) using -the `-pubkey` flag. For detailed instructions, refer to [download encrypted -files](#download-encrypted-files). +encrypted on the server-side by providing a +[public key file](#create-crypt4gh-key-pair) using the `-pubkey` flag. For +detailed instructions, refer to [download encrypted files](#download-encrypted-files). The following options are available for downloading files: