Commit d17cae39 authored by Holger Brandl's avatar Holger Brandl

added cellranger docker notes

parent 3639fda3
## cellranger
https://github.com/mckinsel/cellranger_clean
```bash
PRJ_DATA=~/projects/cellranger
mkdir ${PRJ_DATA}
cd ${PRJ_DATA}
# get some example data
#cp /net/mack/lustre/projects/bioinfo/data/tabler_rnaseq_sc/originals/L23730_Track-55090* .
docker pull marcusczi/cellranger_clean
docker run --rm -ti --name cellranger -v "${PRJ_DATA}":/data marcusczi/cellranger_clean
# process the data https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation
## are bioaries present
cd /data
bcl2fastq --version
#https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/fastq-input
## example data
wget http://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz
tar xvf cellranger-tiny-bcl-1.2.0.tar.gz
wget http://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv
wget http://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-samplesheet-1.2.0.csv
cellranger mkfastq --id=tiny-bcl \
--run=/data/cellranger-tiny-bcl-1.2.0 \\
--csv=/data/cellranger-tiny-bcl-simple-1.2.0.csv
```
via singularity
```bash
##
#singularity shell docker://ubuntu:latest
## intial setup
#mv ~/.singularity /projects/bioinfo/brandl/singularity
#ln -s /projects/bioinfo/$(whoami)/singularity ~/.singularity
# interactive bash shell
srun --partition gpu --pty -n 1 -c 4 --time=1:00:00 --mem-per-cpu=1700 --gres=gpu:0 bash
singularity shell docker://marcusczi/cellranger_clean
# with args
singularity exec docker://marcusczi/cellranger_clean cellranger --help
## with path mapping
# as job
run task zero in pseudo terminal
srun --partition gpu --pty --gres=gpu:0 bash
jl submit -O "--gres=gpu:0" -q gpu "singularity exec docker://marcusczi/cellranger_clean cellranger --help"
jl wait
```
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