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Librarian Query CLI

Queries the Babraham server (or your own!) with supplied FASTQ files and downloads plots.

Librarian CLI 1.3.0
A tool to predict the sequencing library type from the base composition of a supplied FastQ file. Uncompresses .gz files
when reading.

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

FLAGS:
    -h, --help       
            Prints help information

    -l, --local      
            Run all processing locally, replacing the need for a server. Requires Rscript and other dependencies to be
            installed, along with the `scripts` folder. See
            https://github.com/DesmondWillowbrook/Librarian/blob/master/cli/README.md for more details.
            
            This cannot be set together with `--api`.
    -q, --quiet      
            Suppresses all output except errors

        --raw        
            Only output the librarian_heatmap.txt file used by MultiQC, and don't output any plots.
            
            This option requires `local` to be set.
    -V, --version    
            Prints version information


OPTIONS:
        --api <api>                  
            Specifies query URL to send prediction request to. Defaults to Babraham Bioinformatic's server. Passed
            argument is given precedence over environment variable.
            
            This cannot be set together with `--local`. [env: LIBRARIAN_API_URL=]  [default:
            https://www.bioinformatics.babraham.ac.uk/librarian/api/plot_comp]
    -o, --output-dir <output-dir>    
            Output directory (eg. `output_dir/`) [default: ]


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

Installation

CLI binaries can be found in the Github Releases section of the repository.

The released binaries are statically linked with musl, so there shouldn't be too much in the way of system requirements for the CLI except running Linux.

Running with the --local option requires additional dependencies to be installed. Refer to the server README's Runtime Dependencies section for a list of the other dependencies. (The CLI tar file includes a copy of the scripts folder beside the binary)

You might find it useful to refer to the CLI dockerfile for a list of dependencies.

Install from source

Requires a recent version of the Rust toolchain.

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

Querying another server

librarian example.fastq.gz --api http://127.0.0.1:8186/api/plot_comp

To debug the client:

(
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/*
)