|
|
# Use the Transfer Tool
|
|
|
|
|
|
The following commands are available:
|
|
|
- `./spsp auto`- Automatically run the commands to Compress$, Hash, Encrypt & Transfer, add --no-archive option to delete the files after the transfer\ the sent files
|
|
|
- `./spsp auto`- Automatically run the commands to Compress, Hash, Encrypt & Transfer, add --no-archive option to delete the files after the transfer\ the sent files
|
|
|
- `./spsp help` - Shows help screen
|
|
|
- `./spsp test` - Dry run with fake generated files with report
|
|
|
- `./spsp cleanup` - Clean the following directories: logs, sent, viruses, bacteria and .outbox
|
... | ... | @@ -13,7 +13,7 @@ This step assumes that you already followed the guide on [spsp.ch](https://spsp. |
|
|
- Start by **identifying** if your sequences are from **viruses** or **bacteria** (if mixed, you need to separate them)
|
|
|
- Make sure that the sequences described in your metadata file **match** the FASTQ files
|
|
|
- **Create a subfolder** as the date of the day (for example: 26-06-12) **inside bacteria/viruses directory** depending on their type
|
|
|
- **COPY** your FASTQ files and the metadata file inside the freshly created folder
|
|
|
- **COPY** your FASTQ files and the corresponding metadata file inside the freshly created folder
|
|
|
|
|
|
**IT IS VERY IMPORTANT TO ALWAYS PUT YOUR FASTQ FILES AND METADATA FILE INSIDE A SUBFOLDER IN THE BACTERIA/VIRUSES DIRECTORY, OR THE TT WILL IGNORE THE FILES**
|
|
|
|
... | ... | @@ -21,7 +21,7 @@ This step assumes that you already followed the guide on [spsp.ch](https://spsp. |
|
|
|
|
|
If you want to quickly and easily send a batch of FASTQ files with their metadata, just follow those instructions:
|
|
|
|
|
|
- Follow the instruction on [How to prepare FASTQ files with the metadata file](#how-to-prepare-fastq-files-with-the-metadata-file)
|
|
|
- Follow the instructions on [How to prepare FASTQ files with the metadata file](#how-to-prepare-fastq-files-with-the-metadata-file)
|
|
|
- Launch the pipeline by typing `./spsp auto` which will trigger the **automatic** mode
|
|
|
- Once the transfer is over, you should find the sent files (encrypted archive and hash file) in the `sent` folder
|
|
|
|
... | ... | @@ -50,7 +50,7 @@ After the transfer, it shoud look like this: |
|
|
|
|
|
## Use the automatic mode in combination with a CRON task
|
|
|
|
|
|
If you want to use the automatic mode on daily basis, you need to set up a [CRON](https://en.wikipedia.org/wiki/Cron) task.
|
|
|
If you want to use the automatic mode on daily basis without manual user execution, you need to set up a [CRON](https://en.wikipedia.org/wiki/Cron) task.
|
|
|
|
|
|
We recommend the following settings:
|
|
|
|
... | ... | |