|
|
# 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 not keep the sent archives (default behavior)
|
|
|
- `./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
|
|
|
- `./spsp cleanup` - Clean the following directories: logs, sent, viruses, bacteria, and .outbox
|
|
|
|
|
|
## How to prepare FASTQ files with the metadata file
|
|
|
|
|
|
This step assumes that you already followed the guide on [spsp.ch](https://spsp.ch/) and will only tell you how you should orgnaize your files for the Transfer Tool to work properly
|
|
|
This step assumes that you already followed the guide on [spsp.ch](https://spsp.ch/) and will only tell you how you should organize your files for the Transfer Tool to work properly:
|
|
|
|
|
|
- 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
|
... | ... | @@ -62,7 +62,7 @@ This will launch the Transfer Tool at 5 AM every day of the week using the autom |
|
|
|
|
|
In order, this is what happens:
|
|
|
|
|
|
1) Checks that the `.outbox`, `sent`, `viruses`, `bacteria` and `.logs` folders exist.
|
|
|
1) Checks that the `.outbox`, `sent`, `viruses`, `bacteria` and `.logs` folders exist
|
|
|
2) Creates a log file using the current date inside `.logs` directory
|
|
|
3) Checks if the connection to SPSP works
|
|
|
4) Scans the two `viruses` and `bacteria` directories for any folder; if one is found, checks that it contains `.fastq` or `.fastq.gz` and `.xlsx` files at least
|
... | ... | |