This script was initially used to copy our department-level repository to our Cloud server. Not used anymore, but would like to keep for reference. This script makes use of exclude_patterns.txt.
A script to be run on any computer to copy the entire repository on our Cloudserver to that computer. In my case the target directory is synced onto Nextcloud to have maximum backup safety.
Old script to zip all packages for the server. Don't need this anymore, since the HTTP server program is now capable of zipping automatically.
This script can be used like this:
./get_ena_table.py PRJEB39316 -o test.tsv
which downloads a TSV table with meta-info including URLS to download fastq-files in the specified output file (here test.tsv).
This script takes an input poseidon package (-i) and an output file name (-o). It reads the janno of the input package, and applies janno::process_age() to the janno Date_* columns, to calibrate the C14 dates, and fill contextual dates. The output is a new janno file with the calibrated dates.
./janno_calibrate_c14.R [-w/--overwrite] (-i input_poseidon_package_dir) (-o output_janno_file)
When Latitude information is available, the script applies calibration based on IntCal20 or SHCal20 accordingly.
The option -w or --overwrite allows overwriting information in the original janno, otherwise only missing fields are filled-in.