A series of scripts were developed so that users can access imported sequence data and the results of the analysis pipelines. These are referred to as the PathFind or pf scripts. The source code for the Perl module which is used to run the pf scripts can be found on the sanger-pathogens Git repository as Bio-Path-Find.
By the end of this tutorial you can expect to be able to:
This tutorial was created by Victoria Offord.
You can run the commands in this tutorial either directly from the Jupyter notebook (if using Jupyter), or by typing the commands in your terminal window.
If you are using Jupyter, command cells (like the one below) can be run by selecting the cell and clicking Cell -> Run from the menu above or using Ctrl Enter to run the command. Let's give this a try by printing our working directory using the pwd command and listing the files within it. Run the commands in the two cells below.
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pwd
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ls -l
You can also follow this tutorial by typing all the commands you see into a terminal window. This is similar to the "Command Prompt" window on MS Windows systems, which allows the user to type DOS commands to manage files.
To get started, select the cell below with the mouse and then either press control and enter or choose Cell -> Run in the menu at the top of the page.
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echo cd $PWD
Open a new terminal on your computer and type the command that was output by the previous cell followed by the enter key. The command will look similar to this:
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cd /home/manager/pathogen-informatics-training/Notebooks/PathFind/
Now you can follow the instructions in the tutorial from here.
This tutorial assumes that you have Bio-Path-Find installed on your computer.
To be able to access the tutorial dataset, we need to add a few lines to our configuration file which tell it where to write the log file and the location of the tutorial data. We also need to add the paths for our tutorial reference sequences to data/refs.index.
Please run the following commands.
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./setup_config.sh
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./setup_refs.sh
You will be asked to run the following command in each section of the tutorial. This tells the system where to find our configuration file. Please run the command now.
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export PF_CONFIG_FILE=$PWD/data/pathfind.conf
To check that you have installed Bio-Path-Find correctly and that you can access the tutorial, please run the following command:
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pf -h
This should return the help message for the pf scripts.
To get started with the tutorial, head to the first section: Introduction.