Updating the reference libraries from RefSeq

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Core and Tool 4 require reference libraries downloaded from RefSeq. The python scripts automate this process for you and deposit the new library in the reference_libraries folder. You need to update the Tool's config files so that they use the new libraries.

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Making a new library

Reference libraries can easily be made as follows:

1. Navigate to the _maintenance_ folder by entering cd ~/genome_tools/_maintenance_.
2. Run the appropriate script using the command in the table below.
3. Check that the following message appears: Reference library complete.

The commands are:

Reference Library	Command
maxOne	python3 maxOne_phylogeny.py
maxThree	python3 maxThree_taxonomy.py
maxThree (for Tool 4)	python3 maxThree_tool4.py

Reference libraries are automatically saved here:

~/genome_tools/reference_libraries

The newly generated libraries are saved with the current date.

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Linking the Tools to the new library

Update the relevant config files to link the Tools to the newly generated reference libraries by following these three steps:

1. Locate the config file in the File Browser.
2. Double-click on nextflow.config to edit
3. Update the relevent lines (see below), save and close.

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For the Core taxonomy module

The taxonomy module uses the maxThree database.

maxThree has two parts:

• params.fastanidbpath, the reference genome sequences (ending .fasta) and
• params.fastanireflistpath, the names of the reference genomes grouped in files by Genus.

Be sure the update both, replacing YYYY-MM-DD:

params.fastanidbpath = "/file_path/fna_YYYY-MM-DD/*"

params.fastanireflistpath = "/file_path/fna_ref_lists_YYYY-MM-DD/*"

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For the Core phylogeny module

The phylogeny module uses the maxOne database.

The location of the database is specified here:

params.lsbsrrefgenomefasta = "/file_path/fasta_YYYY-MM-DD/"

genomes must end in .fasta.

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For Tool 4

Tool 4 uses the maxOne database.

The location of the database is specified here:

backgroundGenomesDir = "../reference_libraries/tool4_fasta_YYYY-MM-DD"

genomes must end in .fasta.

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