singlem data

The data subcommand downloads (or verifies) the reference data used by SingleM. Once it has been downloaded, the environment variable SINGLEM_METAPACKAGE_PATH can be used to specify the location of the reference data.

Example usage

$ singlem data --output-directory /tmp/dbs
10/12/2022 01:16:04 PM INFO: Downloading ...
10/12/2022 01:21:49 PM INFO: Extracting files from archive...
10/12/2022 01:22:50 PM INFO: Verifying version and checksums...
10/12/2022 01:23:03 PM INFO: Verification success.
10/12/2022 01:23:03 PM INFO: Finished downloading data
10/12/2022 01:23:03 PM INFO: The environment variable SINGLEM_METAPACKAGE_PATH can now be set to /tmp/dbs
10/12/2022 01:23:03 PM INFO: For instance, the following can be included in your .bashrc (requires logout and login after inclusion):
10/12/2022 01:23:03 PM INFO: export SINGLEM_METAPACKAGE_PATH='/tmp/dbs/S3.0.5.metapackage20220806.smpkg.zb'

Then follow the instructions from the final line of above. Set the environment variable so that this data is used automatically, by adding the following to your .bashrc file.

export SINGLEM_METAPACKAGE_PATH='/tmp/dbs/S3.0.5.metapackage20220806.smpkg.zb'

OPTIONS

--output-directory OUTPUT_DIRECTORY

Output directory [required unless SINGLEM_METAPACKAGE_PATH is specified]

--verify-only

Check that the data is up to date and each file has the correct checksum

OTHER GENERAL OPTIONS

--debug

output debug information

--version

output version information and quit

--quiet

only output errors

--full-help

print longer help message

--full-help-roff

print longer help message in ROFF (manpage) format

AUTHORS

Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology
Samuel Aroney, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology
Raphael Eisenhofer, Centre for Evolutionary Hologenomics, University of Copenhagen, Denmark
Rossen Zhao, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology