Getting started¶

1. Synopsis¶

RENEE pipeline can be executed from either using the command line interface (CLI) or graphical user interface (GUI). GUI offers a more interactive way for the user to provide input and adjust parameter settings. This part of the documentation describes how to run renee using the GUI (with screenshots). See Command Line tab to read more about the renee executable and running RENEE pipeline using the CLI.

2. Setting up RENEE¶

# Setup Step 1.) ssh into cluster's head node
# example below for Biowulf cluster
ssh -Y $USER@biowulf.nih.gov

2.2 Grab an interactive node¶

NOTE: Make sure to add --tunnel flag to the sinteractive command for correct display settings. See details here: https://hpc.nih.gov/docs/tunneling/

# Setup Step 2.) Please do not run RENEE on the head node!
# Grab an interactive node first
sinteractive --tunnel  --time=12:00:00 --mem=8gb  --cpus-per-task=4

2.3 Load `ccbrpipeliner` module¶

NOTE: ccbrpipeliner is a custom module created on biowulf which contains various NGS data analysis pipelines developed, tested, and benchmarked by experts at CCBR.

# Setup Step 3.) Add ccbrpipeliner module
module purge # to reset the module environment
module load ccbrpipeliner

If the module was loaded correctly, the greetings message should be displayed.

[+] Loading ccbrpipeliner  6  ... 
###########################################################################
            CCBR Pipeliner release 6
###########################################################################
    "ccbrpipeliner" is a suite of end-to-end pipelines and tools
    Visit https://github.com/ccbr for more details.
    Pipelines are available on BIOWULF and FRCE.
    Tools are available on BIOWULF, HELIX and FRCE.

    The following pipelines/tools will be loaded in this module:

    PIPELINES:
    RENEE       v2.5        https://ccbr.github.io/RENEE/
    XAVIER      v3.0        https://ccbr.github.io/XAVIER/
    CARLISLE    v2.4        https://ccbr.github.io/CARLISLE/
    CHAMPAGNE   v0.3        https://ccbr.github.io/CHAMPAGNE/
    CRUISE      v0.1        https://ccbr.github.io/CRUISE/
    ASPEN       v1.0        https://ccbr.github.io/ASPEN/

    TOOLS:
    spacesavers2    v0.12       https://ccbr.github.io/spacesavers2/
    permfix     v0.6        https://github.com/ccbr/permfix/

###########################################################################
            Thank you for using CCBR Pipeliner
            Comments/Questions/Requests:
            CCBR_Pipeliner@mail.nih.gov
###########################################################################

To check the current version of RENEE, enter:

renee --version

3. Running RENEE¶

3.1 Launching RENEE GUI¶

To run the RENEE pipeline from the GUI, simply enter:

renee gui

and it will launch the RENEE window.

Note: Please wait until window created! message appears on the terminal.

renee_launchscreen

3.2 Folder paths and reference genomes¶

To enter the location of the input folder containing FASTQ files and the location where the results should be created, either simply type the absolute paths

or use the Browse tab to choose the input and output directories

renee_browsePath

renee_enterPath

Next, from the drop down menu select the reference genome (hg38/mm10)

renee_genome

3.3 Submit RENEE job¶

After all the information is filled out, press Submit.

If the pipeline detects no errors and the run was submitted, a new window appears that has the output of a "dry-run" which summarizes each step of the pipeline.

renee_dryrun

Click OK

A dialogue box will popup to confirm submitting the job to slurm.

Click Yes

An email notification will be sent out when the pipeline starts and ends.

4. Special instructions regarding X11 Window System¶

RENEE GUI natively uses the X11 Window System to run RENEE pipeline and display the graphics on a personal desktop or laptop. The X11 Window System can be used to run a program on Biowulf and display the graphics on a desktop or laptop. However, X11 can be unreliable and fail with many graphics applications used on Biowulf. The HPC staff recommends NoMachine (NX) for users who need to run graphics applications.

Please see details here on how to install and connect to Biowulf on your local computer using NoMachine.

Once connected to Biowulf using NX, right click to open a terminal connection

gui_nx_config1

and start an interactive session (with --tunnel flag).

gui_nx_config2

Similar to the instructions above, load the ccbrpipeliner module and enter renee gui to launch the RENEE gui.

gui_nx_renee