A command line client for uploading sequencing metrics from Oxford Nanopore Technologies MinKNOW to a LooseLab minoTour server instance.
MinFQ supports minknow core 4.X.X and 5.X.X as it uses ONT's minknow-api, which is only compatible with said version of MinKNOW-core. So ensure that in the setup.py you edit minknow-api to match the version of minknow-core which can be found in Host Settings -> Software in the minKNOW GUI. If you are the latest version of minKNOW you do not need to do this.
However, base called data can be uploaded from any version of MinKNOW/Guppy.
To install -
.. code-block:: python
pip install minFQ
Example Commands
In the example commands below example parameters are:
- your_user_key: is the long string found in the profile section of your minoTour account.
- url_to_your_minotour_server: Probably 127.0.0.1, could be a remote address like minotour.nottingham.ac.uk
- port_for_your_server: Probably 8000
To monitor both live and fastq data.
.. code-block:: python
minFQ -k [your_user_key] -w /path/to/your/fastq/files -ip 127.0.0.1 -hn
[url_to_your_minotour_server] -p [port_for_your_server]
To monitor just live data from minKNOW.
.. code-block:: python
minFQ -k [your_user_key] -ip 127.0.0.1 -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nf
To monitor live data and enable limited remote control of minKNOW.
.. code-block:: python
minFQ -k [your_user_key] -ip 127.0.0.1 -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nf -rc
To monitor just fastq data.
.. code-block:: python
minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nm
To monitor fastq statistics only. (Note you will not be able to run subsequent analysis on the server which requires sequence data).
.. code-block:: python
minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nm -s
To start an analysis remotely whilst uploading data. Note reference Id may not be required.
.. code-block:: python
minFQ -k [your_user_key] -w /path/to/your/fastq/files -hn [url_to_your_minotour_server]
-p [port_for_your_server] -nm -j [job_id] -r [reference_id]
minFQ Gui
We are in the process of rebuilding a minFQ gui. Watch this space. or probably don't.