Miles Smith milescsmith

Setup jupyter notebook installed in a conda env as a system service:

conda create -n ENV_NAME

conda install jupyter exec-wrappers -n ENV_NAME -c conda-forge

if __name__ == "__main__":
    (from argparse import ArgumentParser[\s\S]*)$(?![\r\n])

print\("([\s\S]+)\{0\}([\s\S]+)"\.format\(([\s\S]+)\),

exFAT support on macOS seems to have some bugs because my external drives with exFAT formatting will randomly get corrupted.

Disk Utility is unable to repair this at first, but the fix is this:

Use diskutil list to find the right drive id.
You want the id under the IDENTIFIER column, it should look like disk1s1
Run sudo fsck_exfat -d <id from above>. eg sudo fsck_exfat -d disk1s3
-d is debug so you'll see all your files output as they're processed.
Answer YES if it gives you the prompt Main boot region needs to be updated. Yes/No?

	docker run \
	-v /home/USER:/workingdir \ # setup access to local folder inside container. Format is ABSOLUTE_LOCAL_PATH:CONTAINER_PATH
	combinelab/salmon \ # maybe one does not always need to do this, but prefix with the container name
	salmon alevin -lISR # run command as usual, using container paths
	-1 /workingdir/LOCAL_FASTQ_SUBDIR/L00#_R1_001.fastq.gz \
	-2 /workingdir/LOCAL_FASTQ_SUBDIR/L00#_R2_001.fastq.gz \
	--chromium \
	-i /workingdir/salmon \
	-p8 \
	-o /workingdir/lane# \

	brew tap caskroom/cask

	brew cask install basictex
	sudo tlmgr update --self
	sudo tlmgr update --all
	sudo tlmgr install titling framed inconsolata

	pip install -e 'git://github.com/{ username }/{ reponame }.git@{ tag name }#egg={ desired egg name }&subdirectory={ subdir }'

	or

	pip install -e 'https://github.com/{ username }/{ reponame }.git@{ branch/tag name }#egg={ whatever }&subdirectory={ subdir }'

	The key is those single quotes - without them, Bash ignores the subdirectory portion.

	library(tidyverse)
	library(lubridate)
	library(ggrepel)

	sars_stats <-
	jsonlite::read_json(
	path = "https://covidtracking.com/api/v1/us/daily.json",
	simplifyVector = TRUE
	) %>%
	as_tibble() %>%

	wsl.exe --shutdown
	cd C:\Users\smithm\AppData\Local\Packages\CanonicalGroupLimited.Ubuntu20.04onWindows_79rhkp1fndgsc\LocalState\
	optimize-vhd -Path .\ext4.vhdx -Mode full