geofetch
command-line usage instructions:
geofetch --help
usage: geofetch [-h] -i INPUT [-n NAME] [-m METADATA_FOLDER] [-f]
[--just-metadata] [-r] [--acc-anno] [--use-key-subset] [-x]
[--config-template CONFIG_TEMPLATE] [-p] [-g GEO_FOLDER]
[-b BAM_FOLDER] [-P PIPELINE_INTERFACES]
Automatic GEO SRA data downloader
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
required: a GEO (GSE) accession, or a file with a list
of GSE numbers
-n NAME, --name NAME Specify a project name. Defaults to GSE number
-m METADATA_FOLDER, --metadata-folder METADATA_FOLDER
Specify a location to store metadata [Default:
$SRAMETA:]
-f, --no-subfolder Don't automatically put metadata into a subfolder
named with project name
--just-metadata If set, don't actually run downloads, just create
metadata
-r, --refresh-metadata
If set, re-download metadata even if it exists.
--acc-anno Also produce annotation sheets for each accession, not
just for the whole project combined
--use-key-subset Use just the keys defined in this module when writing
out metadata.
-x, --split-experiments
Split SRR runs into individual samples. By default,
SRX experiments with multiple SRR Runs will have a
single entry in the annotation table, with each run as
a separate row in the subannotation table. This
setting instead treats each run as a separate sample
--config-template CONFIG_TEMPLATE
Project config yaml file template.
-p, --processed Download processed data [Default: download raw data].
-g GEO_FOLDER, --geo-folder GEO_FOLDER
Optional: Specify a location to store processed GEO
files [Default: $GEODATA:]
-b BAM_FOLDER, --bam-folder BAM_FOLDER
Optional: Specify folder of bam files. Geofetch will
not download sra files when corresponding bam files
already exist. [Default: $SRABAM:]
-P PIPELINE_INTERFACES, --pipeline_interfaces PIPELINE_INTERFACES
Optional: Specify the filepath of a pipeline interface
yaml file. [Default: null]