| from collections import namedtuple | |
| import vaex | |
| import time | |
| import orjson | |
| import os | |
| import psutil | |
| from pyarrow import flight | |
| import pyarrow as pa |
| BootStrap: debootstrap | |
| OSVersion: bionic | |
| MirrorURL: http://us.archive.ubuntu.com/ubuntu/ | |
| %runscript | |
| echo "This is what happens when you run the container..." | |
| %post |
Download reference genome:
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
gunzip GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
mv GCA_000001405.15_GRCh38_no_alt_analysis_set.fna GRCh38.fa
Index reference genome:
bwa index GRCh38.fa
| #!/bin/bash | |
| #Usage: ./vcfmerge.sh {PATH FOR VCFs} a/b/c/ | |
| PICARDPATH=/usr/local/bin | |
| STR="" | |
| for f in ${1}*.dv.vcf.gz | |
| do | |
| if [[ $f != *.dv_merged.vcf.gz ]] |
| BootStrap: debootstrap | |
| OSVersion: trusty | |
| MirrorURL: http://us.archive.ubuntu.com/ubuntu/ | |
| %runscript | |
| echo "This is what happens when you run the container..." | |
| %post | |
| echo "Hello from inside the container" |
| #!/bin/bash | |
| #SBATCH -N 5 | |
| #SBATCH -t 1:10:00 | |
| #SBATCH --ntasks-per-node 1 | |
| #SBATCH --cpus-per-task 16 | |
| #SBATCH --output=sparksingu.out | |
| #SBATCH --mem=50G | |
| ############################ | |
| #For custom configurations python3.6 and Java path |
| BootStrap: debootstrap | |
| OSVersion: bionic | |
| MirrorURL: http://us.archive.ubuntu.com/ubuntu/ | |
| %runscript | |
| echo "This is what happens when you run the container..." | |
| #/home/tahmad/bulk/images/adam.sh | |
| %post |
| #!/bin/bash | |
| #SBATCH -N 5 | |
| #SBATCH -t 1:10:00 | |
| #SBATCH --ntasks-per-node 4 | |
| #SBATCH --cpus-per-task 4 | |
| #SBATCH --output=master6.out | |
| #SBATCH --mem=50G | |
| ############################ | |
| module load pre2019 |