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Installation

install <doc/source/install.rst>_

Upgrading

upgrade <doc/source/upgrade.rst>_

Changelog

changelog <CHANGELOG.rst>_

Running the pipeline

Before you use the pipeline you always need to ensure that the miniconda environment is in your environment's path. You will want to look at the install <doc/source/install.rst>_ for more details

Running a single sample ^^^^^^^^^^^^^^^^^^^^^^^

You can run a single sample by using the runsample.py command. There are 2 examples that you can use. Sample 780 and Sample 947 which are both located in the ngs_mapper/tests/fixtures/functional directory. Inside that directory you will see directory for each sample which contains its reads as well as the reference for each of them and a config file for each sample. You can ignore the config file as it is used by the tests to determine if the sample ran correctly or not

You can use runsample.py on them as follows:

.. code-block:: bash

mkdir -p tdir && cd tdir
runsample -od 780 ../ngs_mapper/tests/fixtures/functional/780{,.ref.fasta} 780
runsample -od 947 ../ngs_mapper/tests/fixtures/functional/947{,.ref.fasta} 947

This will create a temporary directory called tdir and cd into it then run both sample 780 as well as 947 and put their results inside of their own directory named after themselves.

From there you can explore them on your own