Miles Smith milescsmith

The manual for PLINK doesn't exactly show what the format is for the file used to extract or remove particular samples.

The easiest format that works that I know of is

#FID IID
4 MDFL|500511
38 LFRR_303939
62 MDFL|500523
94 LFRR_107325
112 CE_541382

To renew the certificates for the HALO Link server

You first need to find and then kill whatever is currently using port 80
```
netstat -ano | findstr :80
```

In the far right column, there should be a 2-4 digit number. Make a note of that.

SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk MACOSX_DEPLOYMENT_TARGET=12.3 pyenv install 3.9.13

	Auto-start ssh-agent in ZSH

	#tips#wsl#zsh#ssh-agent

	To auto-start the ssh-agent when using zsh add this snippet to your ~/.zshrc:

	if [ $(ps ax \| grep "[s]sh-agent" \| wc -l) -eq 0 ] ; then
	eval $(ssh-agent -s) > /dev/null
	if [ "$(ssh-add -l)" = "The agent has no identities." ] ; then
	# Auto-add ssh keys to your ssh agent

	import gzip
	from functools import partial
	from io import StringIO
	from mimetypes import guess_type
	from pathlib import Path
	from typing import Optional, Union

	from Bio import bgzf

	utils::globalVariables("where")

	tirosh_score_modules <- function(
	expr_obj, # rows == genes, columns == samples
	module_list, # named list
	breaks = 25, # int
	num_ctrls = 100, # int
	parallel = FALSE # bool
	) {

	#! /usr/bin/bash
	find . \
	-type f \
	\( -name ".vcf" -o -name ".vcf.gz" -o -name "*.bcf" \) \
	-printf "%f\n" \
	-exec \
	sh \
	-c
	"bcftools view \
	-H \