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.
- a recent Linux OS that support Docker (see https://www.docker.com/)
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
$ 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]
$ docker run -it --entrypoint="/bin/bash" nmrprocflow/rnmr1d
- Launch Rnmr1D to process a subset of NMR spectra of human urine samples from the MetaboLight MTBLS1 study (http://www.ebi.ac.uk/metabolights/MTBLS1)
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
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/>.