Changes between Initial Version and Version 1 of cypress/Cellranger


Ignore:
Timestamp:
Jul 28, 2020 11:15:11 AM (18 months ago)
Author:
fuji
Comment:

Legend:

Unmodified
Added
Removed
Modified
  • cypress/Cellranger

    v1 v1  
     1= Run Cellranger on Cypress =
     2See [https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome Cellranger Page].
     3
     4== Installation ==
     5==== Setup directory ====
     6suppose you want to install Cellranger into lustre group direcotry, for example '/lustre/project/group/Cellranger'
     7
     8Create the directory
     9{{{
     10export CELLRANGER=/lustre/project/group/Cellranger
     11mkdir $CELLRANGER
     12cd $CELLRANGER
     13}}}
     14
     15And then,
     16[https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_in Follow this page].
     17
     18== Run Cellranger with Cluster Mode ==
     19
     20Copy this and place it in $CELLRANGER/cellranger-4.0.0/external/martian/jobmanagers with file name 'slurm.template'
     21
     22{{{
     23#!/usr/bin/env bash
     24#SBATCH -J __MRO_JOB_NAME__
     25#SBATCH --export=ALL
     26#SBATCH --qos=normal
     27#SBATCH --time=24:00:00
     28#SBATCH --nodes=1 --ntasks-per-node=__MRO_THREADS__
     29#SBATCH --signal=2
     30#SBATCH --no-requeue
     31#SBATCH --mem=__MRO_MEM_GB__G
     32#SBATCH -o __MRO_STDOUT__
     33#SBATCH -e __MRO_STDERR__
     34
     35__MRO_CMD__
     36
     37}}}
     38
     39=== Run Example ===
     40To run the example [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/tutorials/gex-analysis-nature-publication here], create a job script like:
     41
     42{{{
     43#!/bin/bash
     44#SBATCH --qos=normal            # Quality of Service
     45#SBATCH --job-name=normal-master # Job Name
     46#SBATCH --time=24:00:00 # WallTime
     47#SBATCH --nodes=1               # Number of Nodes
     48#SBATCH --ntasks-per-node=1     # Number of tasks (MPI presseces)
     49#SBATCH --cpus-per-task=1       # Number of processors per task OpenMP threads()
     50#SBATCH --gres=mic:0            # Number of Co-Processors
     51#SBATCH --export=ALL
     52#SBATCH --mail-type=ALL
     53#SBATCH --mail-user="USERID"@tulane.edu # YOUR EMAIL ADDRESS
     54
     55
     56
     57# Directory you installed Cellranger
     58export CELLRANGER=/lustre/project/group/Cellranger
     59
     60# Assuming cellranger-4.0.0
     61export PATH=$CELLRANGER/cellranger-4.0.0:$PATH
     62
     63cellranger count --id=normal \
     64                 --transcriptome=$CELLRANGER/refdata-gex-mm10-2020-A \
     65                 --fastqs=./indepth_C05_MissingLibrary_1_HL5G3BBXX,./indepth_C05_MissingLibrary_1_HNNWNBBXX \
     66                 --jobmode=slurm \
     67                 --localmem=128 \
     68                 --localcores=20 \
     69                 --maxjobs=8 \
     70                 --jobinterval=1000
     71}}}
     72
     73With this script, 'cellranger' submits at most 8 sub-jobs. You can set the maximum number of jobs by changing:
     74
     75{{{
     76                 --maxjobs=18 \
     77}}}
     78 
     79This will take less than 6 hours on Cypress.