GPSW commands#

Version#

To display the GPSW version:

$ gpsw --version
gpsw 0.9.2

Help#

To display the GPSW help message, use the --help option. This will show you the available sub-commands and options for GPSW. The help message provides a brief overview of the tool and its functionalities:

$ gpsw --help
usage: gpsw [-h] [--version] {fetch,run} ...

GPSW: A tool for analysing and processing Global Protein Stability Profiling
data.

positional arguments:
  {fetch,run}  Sub-command help

options:
  -h, --help   show this help message and exit
  --version    show programs version number and exit

GPSW fetch#

The sub-command fetch is used to download the GPSW code and analysis-specific configuration files from a specific release on GitHub:

$ gpsw fetch --help
usage: gpsw fetch [-h] [-t TAG] [--test-data] [-d DIRECTORY]

Fetch GPSW code from a specific release from https://github.com/niekwit/gps-
orfeome.

options:
  -h, --help            show this help message and exit
  -t TAG, --tag TAG     Release tag of the code to download (default: latest)
  --test-data           Include test data in the download (and relating config
                        and resources directories)
  -d DIRECTORY, --directory DIRECTORY
                        Directory to download the code to target directory
                        (default: current directory)

Note

If you specify the TAG as anything other than latest and 0.6.3 or earlier, make sure that the gpsw conda environment was made with the same version of GPSW. For example, if you want to use the 0.6.3 release, you should create the conda environment with the command:

$ conda create -n gpsw bioconda::gpsw=0.6.3 pandas=2.2.3 pygments=2.19.1

GPSW run#

The sub-command run is used to run the GPSW pipeline and create a report:

$ gpsw run --help
usage: gpsw run [-h] [-p PROFILE] [--snakemake-args SNAKEMAKE_ARGS] [-d] [-q]

Run the GPSW pipeline and create report.

options:
  -h, --help            show this help message and exit
  -p PROFILE, --profile PROFILE
                        Path to Snakemake profile YAML file (only has to be
                        provided at first run) (OPTIONAL, use value None for
                        no profile)
  --snakemake-args SNAKEMAKE_ARGS
                        Extra Snakemake arguments (should be '"double-
                        quoted"')
  -d, --dry-run         Dry-run workflow only
  -q, --quiet           Run GPSW quietly
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