This is Rust code to update Wikidata items from GeneDB GFF and GAF files.

Installation

1. Install Rust (it's a one-liner)
2. git clone https://github.com/sanger-pathogens/genedbot.git
3. cd genedbot
4. cargo build --release
5. Create a bot.ini file, like so:

[user]
user = GeneDBot
pass = INSERT_PASSWORD_HERE
proxy = http://wwwcache.sanger.ac.uk:3128

Usage:

1. As pathpipe@pathpipe-farm4, in ~/genedbot directory
2. ./target/release/genedbot SPECIES_CODE (SPECIES_CODE eg Pfalciparum), or
3. ./target/release/genedbot all to run all species sequentially (use run_all.sh to start this via bsub on farm4), or
4. ./target/release/genedbot --help for options

Update

1. As pathpipe@pathpipe-farm4, in ~/genedbot directory
2. git pull ; rustup update ; cargo update ; cargo build --release