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How to Get and Set Up GAME

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Diego De Panis edited this page May 26, 2026 · 4 revisions

1) Get the latest version

GAME is adding features rapidly, so please download the latest release (or clone the repo for getting hot fixes faster!)

2) Create the GAME Conda Environment

The environment contains Snakemake packages and NomNom. Enter the GAME folder and:

conda env create -f install.yml

3) Enter Your Data in a Table

You can use Google Drive, Excel, LibreOffice, Numbers, CSV, TSV, etc.

The table should contain these columns:

sp_name asm_id asm_file asm_ssex_chr sample_id sample_sex_karyo read_type read_files

Please see the example table. The easiest is to make a copy of that Google table (File->Make a copy) and replace the fields with your data. Remember to change permissions (Share-> change General access to "Anyone with the link" viewer)

Column Descriptions:

  • sp_name: Species name in binomial nomenclature (e.g., Vultur gryphus)
  • asm_id: Assembly identifier (e.g., hifiasm_l2, yahs_test, or ASM2260516v1)
  • asm_files: Path to reference assembly file, URL, or accession number (e.g., GCA_022605165.1). If it's a link or accession, the pipeline will download the data automatically.
  • asm_sex_chr: Comma-separated list of name of the sex chr contigs, or empty (e.g., CM075625.1, CM075626.1)
  • sample_id: Sample identifier (e.g., indiviual_39, SAMEA13793175)
  • sample_sex_karyo: sample_sex_karyo (must be identical on every row sharing the same sample_id) Sex-chromosome karyotype of the individual. E.g., ZW, XY, X0, Z0, XY1Y2, X1X2Y (for heterogametics), ZZ, XX, X1X1X2X2, Z1Z1Z2Z2 (for homogametics) or any empty/empty-like value such as None, NA, - (for unknowns). Must be identical on every row sharing the same sample_id
  • read_type: Can be illumina, 10x, hifi, or ont (variations like PacBio, paired-end, linked-read, arima, promethion and others should also work fine)
  • read_files: Comma-separated list of paths to read files. Can also be accession numbers (e.g., ERR12205285,ERR12205286). For paired-end reads, list as: forward1,reverse1,forward2,reverse2. Also can use pattern expansion in paths, like /readsA/*.fq.gz, /readsB/*.fq.gz

4) Configure the Control Panel

Add the table path/address and select different options in:

config/control_panel.yaml

5) Configure Cluster or Computer Parameters

Depending on which mode you will run, configure the respective parameters in the config file. Important: Don't forget to bind the folders in the apptainer-args field.

GAME/execution/
├── local/
│   └── config.yaml
└── slurm/
    └── config.yaml

Note: You can tweak per-tool resources boundaries in GAME/config/resources.yaml

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