Add installation instructions for databases

[oflyncia]

Hey,

Do you have any pre-built databases hosted anywhere?

I can see in the tutorial rep82: "data/references/rep82" is it possible to have access to this ?

Thanks

Ciaran

[bhillmann]

Yes, those do exist currently on Amazon S3.

You can download them by running the command on the file shogun_db_links.txt.

wget -i <input file>

[jgarbe256]

wget -i shogun_db_links.txt doesn't get the downloaded files into the directory structure shogun expects. This will download the files into the correct structure:

wget https://s3.us-east-2.amazonaws.com/shogun-db/metadata.yaml -P shogun-db wget https://s3.us-east-2.amazonaws.com/shogun-db/rep82.fna -P shogun-db wget https://s3.us-east-2.amazonaws.com/shogun-db/rep82.tax -P shogun-db wget https://s3.us-east-2.amazonaws.com/shogun-db/sheared_bayes.txt -P shogun-db wget https://s3.us-east-2.amazonaws.com/shogun-db/utree/rep82.gg.ctr -P shogun-db/utree wget https://s3.us-east-2.amazonaws.com/shogun-db/utree/rep82.gg.log -P shogun-db/utree wget https://s3.us-east-2.amazonaws.com/shogun-db/function/ko-enzyme-annotations.txt -P shogun-db/function wget https://s3.us-east-2.amazonaws.com/shogun-db/function/ko-module-annotations.txt -P shogun-db/function wget https://s3.us-east-2.amazonaws.com/shogun-db/function/ko-pathway-annotations.txt -P shogun-db/function wget https://s3.us-east-2.amazonaws.com/shogun-db/function/ko-species2ko.80pct.txt -P shogun-db/function wget https://s3.us-east-2.amazonaws.com/shogun-db/function/ko-species2ko.txt -P shogun-db/function wget https://s3.us-east-2.amazonaws.com/shogun-db/function/ko-strain2ko.txt -P shogun-db/function wget https://s3.us-east-2.amazonaws.com/shogun-db/filter/humanD252.edx -P shogun-db/filter wget https://s3.us-east-2.amazonaws.com/shogun-db/filter/humanD252.acx -P shogun-db/filter wget https://s3.us-east-2.amazonaws.com/shogun-db/burst/rep82.edx -P shogun-db/burst wget https://s3.us-east-2.amazonaws.com/shogun-db/burst/rep82.acx -P shogun-db/burst wget https://s3.us-east-2.amazonaws.com/shogun-db/bt2/rep82.1.bt2l -P shogun-db/bt2 wget https://s3.us-east-2.amazonaws.com/shogun-db/bt2/rep82.2.bt2l -P shogun-db/bt2 wget https://s3.us-east-2.amazonaws.com/shogun-db/bt2/rep82.3.bt2l -P shogun-db/bt2 wget https://s3.us-east-2.amazonaws.com/shogun-db/bt2/rep82.4.bt2l -P shogun-db/bt2 wget https://s3.us-east-2.amazonaws.com/shogun-db/bt2/rep82.rev.1.bt2l -P shogun-db/bt2 wget https://s3.us-east-2.amazonaws.com/shogun-db/bt2/rep82.rev.2.bt2l -P shogun-db/bt2