2. Installing

Requirements

Software dependencies

Java 8, Nextflow and Docker (or Singularity if using high-performance computing) are required for this software

Environment requirements for using RUMP on private computer

RUMP can be run in any UNIX-like (e.g., Linux and MacOS) system. For Windows user, virtual machine (e.g., https://www.virtualbox.org/) is needed if using RUMP on private computer;MobaXTerm can be used without the need of virtual machine if running RUMP with high-performance computing.

Steps

1. Direct to the folder you want to save the project. (<1s) cd command should be used for this, If you have no idea what cd is, please read https://linuxize.com/post/linux-cd-command/. For example, I usually save all my projects in folder /blue/djlemas/xinsongdu/jupyter_notebook/projects/, then I should type the following:

cd /blue/djlemas/xinsongdu/jupyter_notebook/projects/

2. Clone this repository (5m):

git clone https://github.com/lemaslab/RUMP.git

3. Move into the repository directory (<1s):

cd rump

4. Remove README.md files from data folders (<1s):

rm data/POS/README.md data/NEG/README.md

Folder Layout

.
├── Dockerfile
├── LICENSE
├── MZmine-2.53-Linux
│   ├── bin
│   ├── conf
│   ├── legal
│   ├── lib
│   ├── log
│   ├── manual.pdf
│   └── startMZmine-Linux
├── Negative_Garrett_MetaboliteStd_Library_RP_edited01152019JG.csv
├── Positive_Garrett_MetaboliteStd_Library_RP_edited01152019JG.csv
├── README.md
├── accessibility.properties
├── clear.sh
├── data
│   ├── NEG
│   ├── POS
│   └── README.md
├── figs
│   ├── Metabolomics\ Pipeline.jpeg
│   ├── Metabolomics\ Pipeline_V2.png
│   ├── Metabolomics_Pipeline_V3.png
│   ├── Metabolomics_Pipeline_V4.png
│   ├── MultiQC_screenshot.png
│   ├── design_file_format.png
│   ├── nextflow_report.html
│   ├── nextflow_report_1.png
│   ├── nextflow_report_2.png
│   ├── pipeline.png
│   ├── pipeline_old.png
│   ├── reproducibility_test.png
│   └── workflow.pptx
├── functional_test
│   ├── sample_Nextflow_outputs
│   ├── sample_data
│   └── sample_results
├── logs
│   ├── README.md
│   └── success_report.txt
├── main.nf
├── nextflow.config
├── r_package_install.R
├── results
│   ├── README.md
│   ├── figs
│   ├── mqc
│   ├── mummichog
│   └── peak_table
├── rump
│   ├── add_stats.py
│   ├── bar_plot.py
│   ├── batchfile_generator_neg_253.py
│   ├── batchfile_generator_pos_253.py
│   ├── blank_subtraction.py
│   ├── data_info.py
│   ├── h_clustering.py
│   ├── input_check.py
│   ├── multiqc_config.yaml
│   ├── mummichog_input_prepare.py
│   ├── pca.py
│   ├── peak_number_comparison.py
│   ├── software_descriptions_mqc.txt
│   ├── unit_test.py
│   ├── unknown_search.R
│   └── venn.py
└── run_aftermzmine.nf