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shubham1637 / DIAlignR

This is a R package for alignment of DIA mass-spec data
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Docker image for running CLI for alignTargetedRuns + Snakemake workflow #18

Closed singjc closed 2 years ago

singjc commented 3 years ago

Docker

Pull image

docker push singjust/dialignr:2.0.0

Build image

docker build --no-cache -t singjust/dialignr:2.0.0 .

Run Command

$docker run -it --rm -v `pwd`:/data singjust/dialignr:2.0.0

Name: 
        Run DIAlignR's alignTargetedRuns via the Command Line

    Usage: 
        Rscript alignTargetedRuns_cli.R --dataPath=/data/ [args] | --help

        Example: Rscript alignTargetedRuns_cli.R --dataPath=/data/osw/ --params=context:experiment-wide,maxFdrQuery:0.01

        Example2: Rscript alignTargetedRuns_cli.R --dataPath=/data/osw/ --oswMerged=FALSE --params=context:experiment-wide,maxFdrQuery:0.01 --runs=run0,run1,run2 --peps=0,1 --applyFun=BiocParallel::bplapply --regBioCP=BiocParallel::register(BiocParallel::MulticoreParam(workers=4,progressbar=TRUE))

    Options: 
        --dataPath: path to xics and osw directory.
        --outFile: name of the output file.
        --oswMerged: TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
        --params: Parameters for the alignment functions generated from DIAlignR::paramsDIAlignR(). Separate keys and values using a ':', and separate parameters using ','. Example: --params=context:experiment-wide,maxFdrQuery:0.01,fitEMG:TRUE
        --runs: names of xics file without extension. Separate runs using ','. Example: --runs=run0,run1,run2
        --refRun: reference for alignment. If no run is provided, m-score is used to select reference run.
        --peps: ids of peptides to be aligned. If NULL, align all peptides. Separate peptide ids using ','. Example--peps=1,2,3
        --appyFun: value must be either lapply or BiocParallel::bplapply.
        --regBioCP: If using BiocParallel::bplapply, register cores to use. Example: --regBioCP=BiocParallel::register(BiocParallel::MulticoreParam(workers=4,progressbar=TRUE)) . Make sure there are no spaces in this command
        --help: Display this help message

Example

docker run -it --rm -v `pwd`:/data singjust/dialignr:2.0.0 --dataPath=/data/ --outFile=/data/dialignr

Snakemake workflow

To run the snakemake workflow, you need to ensure you have snakemake and singularity installed.

To change parameters for your experiment, edit the input, output and parameters in the snakemake/Snakefile.dialignr file.

Run Command

$cd snakemake
$bash cmd.sh