Configurations

Using Dagster to run synphage pipeline allows the user to easily configure the jobs at run-time when required.

User data directory

Warning

Only valid when synphage is installed with pip.

The path is normally set as an environment variable INPUT_DIR, but the directory can be modified at run time from the job configuration panel, accessible through the Open Launchpad button.

Field Name	Description	Default Value
input_dir	directory to the users' GenBank files	INPUT_DIR or TEMP_DIR

Query config options

To change the query configations, open the dropdown menu at the right of the Materialize all black button. Then go to Open launchpad. This will open a pop-up window with the configurations.

Field Name	Description	Default Value
search_key	Keyword(s) for NCBI query	Myoalterovirus

Plot config options

To change the plot configations, open the dropdown menu at the right of the Materialize all black button. Then go to Open launchpad. This will open a pop-up window with the configurations.

List of the supported configurations:

1. Genome selection

   Field Name	Description	Default Value
   sequence_file	File containing the plot instruction	sequences.csv

2. Graphic

   Field Name	Description	Default Value
   title	Generated plot file title	synteny_plot
   graph_type	Type of dataset to use for the graph	blastn
   colours	Gene identity colour bar	["#fde725", "#90d743", "#35b779", "#21918c", "#31688e", "#443983", "#440154"]
   gradient	Nucleotide identity colour bar	#B22222
   graph_shape	Linear or circular representation	linear
   graph_pagesize	Output document format	A4
   graph_fragments	Number of fragments	1
   graph_start	Sequence start	1
   graph_end	Sequence end	length of the longest genome