= Run Cellranger on Cypress =
See [https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome 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,
[https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_in 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 [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/tutorials/gex-analysis-nature-publication 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.