RUMP Personal Computer Documentation
posted on May 21, 2020

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Asciinema Tutorial for Running RUMP: https://asciinema.org/a/CqZ9KjtP42oqMoeAXYKAmMjv3

It may take around 8 hours to run. You can copy this command for step 14.

1. Install Ubuntu desktop.

2. Install VirtualBox.

3. Install Ubuntu inside the VirtualBox. When selecting memory size, choose 7000 MB. When selecting file size, choose at least 40 GB. Move into settings, select System, and then Processor. Allocate 4 CPUs. If your computer is running extremely slowly in the VirtualBox, change to 2 CPUs. When you close the VirtualBox, always select “Power off the machine”.

4. Start Ubuntu. Open terminal with ctrl + alt + T.

5. Clone RUMP repository.

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

6. Move into RUMP repository.

   $ cd RUMP
   

7. Install curl command.

   $ sudo apt update
   $ sudo apt upgrade
   $ sudo apt install curl
   

8. Install git command.

   $ sudo apt install git-all
   

9. Install Docker.

10. Install Java.

    $ sudo apt-get update
    $ sudo apt-get install default-jre
    

11. Install Nextflow.

12. Download MZmine-2.53 into the repository.

    wget https://github.com/mzmine/mzmine2/releases/download/v2.53/MZmine-2.53-Linux.zip && unzip MZmine-2.53-Linux.zip && rm MZmine-2.53-Linux.zip
    

13. Access “nextflow.config”. Hover over “7GB”, type “r”, and “4”. This will change “7GB” to “4GB” for memory storage. Repeat for the other “7GB”. Hit esc upon completion. Type “:wq” to save changes and exit the file.

    vi nextflow.config
    

14. Test RUMP with sample data provided.

    ./nextflow main.nf --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 -with-docker xinsongdu/lemaslab_rump:v0.0.0