budsonjelmont’s gists

budsonjelmont / fix_commit_history_because_you_commited_using_the_wrong_username_or_email.sh

Created June 9, 2025 13:31

Fix git commit history in your local because you committed with the wrong username or email

	# Requires uvx https://docs.astral.sh/uv/guides/tools/#running-tools
	# Run command below to fix the commits in your local, then force push
	# to remote.
	uvx git-filter-repo --commit-callback '
	if commit.author_name != b"budsonjelmont" or commit.author_email != b"[email protected]":
	commit.author_name = b"budsonjelmont"
	commit.author_email = b"[email protected]"
	commit.committer_name = b"budsonjelmont"
	commit.committer_email = b"[email protected]"
	'

budsonjelmont / troubleshooting_docker_dns.sh

Created September 18, 2024 20:24

Minimal example for confirming that docker containers can DNS resolve other containers by name as well as external URLs. Based on the Docker networking tutorial here: https://docs.docker.com/engine/network/tutorials/standalone/

	set -x

	# Create resources
	docker network create --driver bridge alpine-net
	docker run -dit --name alpine1 --network alpine-net alpine ash
	docker run -dit --name alpine2 --network alpine-net alpine ash
	docker network inspect alpine-net

	# Test connectivity
	docker exec -t alpine1 ping -c 3 alpine2

budsonjelmont / create_omics_annot_store_import_policy_and_role.py

Created March 29, 2024 20:49

Create a role that can import into Omics analytics stores

	import boto3
	import json

	region = "us-east-1"
	account_id = 666666666666

	policy = {
	"Version": "2012-10-17",
	"Statement": [
	{

budsonjelmont / import_gnomad_vcfs_to_aws_omics_annot_store.py

Last active March 29, 2024 20:49

Batch import gnomAD VCFs into an Omics annotation store

	import boto3

	dataset = 'genomes'
	semver = '2.1.1'
	import_arn = 'arn:aws:iam::[account_id]:role/service-role/[role_name]'

	annot_store_name='gnomad_grch37'
	annot_store_version_name= dataset + '_v' + str(semver).replace('.','_')

	base_s3_uri = 's3://gnomad-public-us-east-1/release/' + str(semver) + '/vcf/' + dataset

budsonjelmont / gtf2bed.py

Last active October 15, 2019 19:37 — forked from davidliwei/gtf2bed.py

Converting Cufflinks predictions (.GTF) into .BED annotations

	#!/usr/bin/env python3
	'''
	gtf2bed.py converts GTF file to BED file.
	Usage: gtf2bed.py {OPTIONS} [.GTF file]
	History
	Nov.5th 2012:
	1. Allow conversion from general GTF files (instead of only Cufflinks supports).
	2. If multiple identical transcript_id exist, transcript_id will be appended a string like "_DUP#" to separate.
	'''