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Librarian Query CLI

Queries the Babraham server with supplied FASTQ files and downloads plots.

Librarian CLI 1.0.0
A tool to predict the sequencing library type from the base composition of a supplied FastQ file. Uncompresses .gz files
when reading.

USAGE:
    librarian [OPTIONS] <input>...

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
    -o, --output <outdir>    Output path

ARGS:
    <input>...    List of input files

Install from source

Requires a recent version of the Rust toolchain.

cargo install --git "https://github.com/DesmondWillowbrook/Librarian/" cli

Querying another server

(
export LIBRARIAN_API_URL=http://127.0.0.1:8186/api/plot_comp
export RUST_LOG=trace # other values are `debug`, `info`, `warn` and `error` - default is `info`
cargo run --release --bin librarian -- PATH_TO_INPUT
)

For example, to pass the example files, first uncompress with unzip example_inputs.zip in ../frontend/example_inputs/ and then run

(
export LIBRARIAN_API_URL=http://127.0.0.1:8186/api/plot_comp
export RUST_LOG=trace # other values are `debug`, `info`, `warn` and `error` - default is `info`
cargo run --release --bin librarian -- ../frontend/example_inputs/example_inputs/*
)