Processing scripts for The Microsetta Initiative
This repository houses the scripts that process Microsetta data. The output from processing can be served by the microsetta-public-api, allowing participants to access and explore their data. These outputs include alpha and beta diversity, as well as taxonomy details.
The processing scripts depend on a standard QIIME 2 environment, and redbiom, and assume a Torque/PBS submission environment.
A set of environment variables control the processing:
$QIIME_VERSIONis used onconda activate(e.g., 2020.11). [REQUIRED]$EMAILis a contact email to specify on job submission. [OPTIONAL]$TMI_NAMEis a shortname for the processing run (e.g., tmi-gut-16S) [REQUIRED]$TMI_TITLEis a human readable longname (e.g., "Microsetta fecal 16S data") [REQUIRED]$TMI_DATATYPEspecifies whether to process 16S or WGS [REQUIRED]$STUDIEScontains a dot delimited list of Qiita study IDs to process. For example, "10317.850"is the combination of the American Gut (Microsetta) data and the data from Yatsunenko et al Nature 2012. [REQUIRED]$ENV_PACKAGEcontains a dot delimited list of EBIenv_packagevalues to process (e.g., "human-gut") [REQUIRED]$AG_DEBUG, if set to true, limits processing to 1000 samples [OPTIONAL]$TMI_WEIGHTED_UNIFRAC, if set, compute weighted unifrac in addition to unweighted [OPTIONAL]$TMI_SINGLE_SUBJECT, if set, provide various outputs over an individual subject rather than all samples [OPTIONAL]
If running submit_all.sh directly, or one of the individual scripts, it is necessary to specify the above required environment variables.
Alternatively, the reprocess.sh script can be used which sets many of the variables above followed by executing submit_all.sh. If using reprocess.sh, it is still necessary to indicate $QIIME_VERSION.