Aaron Holmes aholmes

Software engineer working in cancer research.

ckandoth / ngs_test_data.sh

Last active February 17, 2025 09:10

Create test data for CI/CD of a FASTQ to gVCF bioinformatics pipeline

	# GOAL: Create test data for CI/CD of a germline variant calling pipeline (FASTQ to gVCF)

	# Steps below were performed on Ubuntu 24.04, but should be reproducible on any Linux distro

	# Download and install micromamba under your home directory and logout:
	"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

	# Log back in to add micromamba to your $PATH, and then use it to install the tools we need:
	micromamba create -y -n bio -c conda-forge -c bioconda htslib==1.21 samtools==1.21 bcftools==1.21 picard-slim==3.3.0
	micromamba activate bio

endolith / Has weird right-to-left characters.txt

Last active April 29, 2025 03:07

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