Changes between Initial Version and Version 1 of cypress/Cellranger

Timestamp:

07/28/20 11:15:11 (5 years ago)

Author:

fuji

Comment:

—

cypress/Cellranger

@@ +1 @@
+= 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 \
+                 --localmem=128 \
+                 --localcores=20 \
+                 --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.