wiki:cypress/Cellranger

Version 2 (modified by cbaribault, 8 months ago) (diff)

In cluster mode example, removed superfluous options —localmem and —localcores

Run Cellranger on Cypress

See Cellranger Page.

Installation

Setup directory

suppose you want to install Cellranger into lustre group direcotry, for example '/lustre/project/group/Cellranger'

Create the directory

export CELLRANGER=/lustre/project/group/Cellranger
mkdir $CELLRANGER
cd $CELLRANGER

And then, Follow this page.

Run Cellranger with Cluster Mode

Copy this and place it in $CELLRANGER/cellranger-4.0.0/external/martian/jobmanagers with file name 'slurm.template'

#!/usr/bin/env bash
#SBATCH -J __MRO_JOB_NAME__
#SBATCH --export=ALL
#SBATCH --qos=normal
#SBATCH --time=24:00:00
#SBATCH --nodes=1 --ntasks-per-node=__MRO_THREADS__
#SBATCH --signal=2
#SBATCH --no-requeue
#SBATCH --mem=__MRO_MEM_GB__G
#SBATCH -o __MRO_STDOUT__
#SBATCH -e __MRO_STDERR__

__MRO_CMD__

Run Example

To run the example here, create a job script like:

#!/bin/bash
#SBATCH --qos=normal		# Quality of Service
#SBATCH --job-name=normal-master # Job Name
#SBATCH --time=24:00:00	# WallTime
#SBATCH --nodes=1 		# Number of Nodes
#SBATCH --ntasks-per-node=1 	# Number of tasks (MPI presseces)
#SBATCH --cpus-per-task=1 	# Number of processors per task OpenMP threads()
#SBATCH --gres=mic:0  		# Number of Co-Processors
#SBATCH --export=ALL
#SBATCH --mail-type=ALL
#SBATCH --mail-user="USERID"@tulane.edu # YOUR EMAIL ADDRESS



# Directory you installed Cellranger
export CELLRANGER=/lustre/project/group/Cellranger

# Assuming cellranger-4.0.0
export PATH=$CELLRANGER/cellranger-4.0.0:$PATH

cellranger count --id=normal \
                 --transcriptome=$CELLRANGER/refdata-gex-mm10-2020-A \
                 --fastqs=./indepth_C05_MissingLibrary_1_HL5G3BBXX,./indepth_C05_MissingLibrary_1_HNNWNBBXX \
		 --jobmode=slurm \
          	 --maxjobs=8 \
                 --jobinterval=1000

With this script, 'cellranger' submits at most 8 sub-jobs. You can set the maximum number of jobs by changing:

          	 --maxjobs=18 \

This will take less than 6 hours on Cypress.

Note: To avoid unnecessary runtime warnings in cluster mode, do not specify options —localmem and —localcores, since they only apply to local mode. See output from the command cellranger count -h for details.