popscle
Link to section 'Introduction' of 'popscle' Introduction
Popscle is a suite of population scale analysis tools for single-cell genomics data.
Docker hub: https://hub.docker.com/r/cumulusprod/popscle and its home page on Github.
Link to section 'Versions' of 'popscle' Versions
- 0.1b
Link to section 'Commands' of 'popscle' Commands
- popscle
Link to section 'Module' of 'popscle' Module
You can load the modules by:
module load biocontainers
module load popscle
Link to section 'Example job' of 'popscle' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Popscle on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=popscle
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers popscle
popscle dsc-pileup --sam data/$bam --vcf data/$ref_vcf --out data/$pileup