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Rnmr1D

Version 1.2.22

Rnmr1D is the main module in the NMRProcFlow web application (http://nmrprocflow.org) concerning the NMR spectra processing.

  • Inside NMRProcFlow, Rnmr1D allows users to process their NMR spectra within a GUI application and thus the macro-command sequence coming from this process can be saved.

  • Outside NMRProcFlow Rnmr1D become a CLI application allowing users to replay the macro-command sequence generated within NMRProcFlow. Moreover, without using NMRProcFlow, this module can also be used to replace any 'home-made script' by a macro-command sequence.

Installation

Requirements:

You need to have the docker image 'rnmr1d' into your local docker library. For that, two ways are possible:

  • You have to create the docker image:

    Step 1: Clone this repository, then `cd` to your clone path.
    
        $ git clone https://bitbucket.org/nmrprocflow/rnmr1d
        $ cd rnmr1d
    
    Step 2: Create the docker image:
    
        $ docker build -t docker.io/nmrprocflow/rnmr1d:latest .
    
  • You can simply pull the docker image from docker hub:

        $ docker pull docker.io/nmrprocflow/rnmr1d
    

Then, you should have something like below:

$ docker images
REPOSITORY                      TAG                 IMAGE ID            CREATED             SIZE
docker.io/nmrprocflow/rnmr1d    latest              ba210fb561e4        31 minutes ago      1.13 GB

Usage:

$ docker run -it --rm nmrprocflow/rnmr1d --help
Rnmr1D - Command Line Interface (CLI) of the NMR spectra processing module (R package 'Rnmr1D')

Usage:
  Rnmr1D [options]

Options:
  -h, --help               Show this screen.
  -d, --debug              Show more information
  -r, --recover            Recover a previous session specified by the outdir (o) option
  -i, --input <path|file>  The full path of either the raw spectra directory or the ZIP file of raw spectra
      --only <name>        Process only one entry specified by a name of either a nmrML or folder under the input directory.
                           In that case, the input value must be a full path of a directory
  -s, --samples <file>     The full path name of the Sample file (tabular format)
  -p, --proccmd <file>     The full path name of the Macro-commands file for processing (text format)
  -b, --bucfile <file>     The full path name of the file of bucket's zones (tabular format)
  -n, --outnorm <type>     Normalization method. Possible values are: none, CSN, PQN [default: none]
  -c, --cpu <n>            The number of cores [default: maximum of the machine]
  -o, --outdir <path>      The full path name of the directory to output the resulting files
  -e, --export <format>    Export spectra data in Text format; Possible formats are: CSV, TSV [default: none]
  -l, --logfile <file>     The full path name of the LOG file [default: stdout]

Bash Shell

$ docker run -it --entrypoint="/bin/bash" nmrprocflow/rnmr1d

Example

docker run -i --rm -v `pwd`/examples:/data nmrprocflow/rnmr1d --debug  \
   --input   /data/input/MTBLS1/ADG1.zip \
   --proccmd /data/input/MTBLS1/NP_macro_cmd_MTBLS1.txt \
   --outnorm PQN \
   --outdir /data/output/ADG1 | tee ./examples/output/ADG1/stdout.log

See a more detailled example

License

Copyright (C) 2017 Daniel Jacob - INRA

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.