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3. Setup projects with RUMP using local machine
Xinsong Du edited this page Feb 10, 2021
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replace /ufrc/djlemas/xinsongdu/jupyter_notebook/projects/RUMP/
with the location on your own machine
cd /ufrc/djlemas/xinsongdu/jupyter_notebook/project/RUMP/
nextflow main.nf -profile docker --input_dir_pos functional_test/sample_data/POS/ --input_dir_neg functional_test/sample_data/NEG --POS_design_path functional_test/sample_data/pos_design.csv --NEG_design_path functional_test/sample_data/neg_design.csv
Sample outputs of MZmine are provided directly, and processes regarding using MZmine to process raw data, which are the most time-consuming processes, will be skipped.
nextflow run_aftermzmine.nf -profile docker --input_dir_pos functional_test/sample_data/POS/ --input_dir_neg functional_test/sample_data/NEG --POS_design_path functional_test/sample_data/pos_design.csv --NEG_design_path functional_test/sample_data/neg_design.csv --pos_mzmine_peak_output functional_test/sample_results/peak_table/pos_data_before_blank_subtraction.csv --neg_mzmine_peak_output functional_test/sample_results/peak_table/neg_data_before_blank_subtraction.csv
Use RUMP to process your own data. (See executing time estimation)
- Save your positive data files (.mzXML format) to
data/POS/
and negative data todata/NEG/
- Create design files for positive data and negative data, indicating the group of each file, save them to
data/pos_design.csv
anddata/neg_design.csv
. Sample design file can be found indata/sample_data/pos_design.csv
anddata/sample_data/neg_design.csv
- Execute RUMP
nextflow main.nf -with-docker xinsongdu/lemaslab_rump:v1.0.0
Usage
- Setup your computer
- Installing
- Setup your projects with RUMP using local machine
- Setup your projects with RUMP using HiPerGator
- Setup your projects with RUMP using Amazon Web Service
- Executing time estimation
- Data processing parameters modification
Components
- Data collection/generation
- MODIS data quality control
- Data format conversion
- Data processing
- File format transformation
- Statistical analysis
- Unidentified metabolites search
- Pathway analysis
- Report generation
Developers