MVesuviusC

while read line
do 
	echo "$line"
done < misc/inputfile.txt

MVesuviusC

theme_set(theme_bw())

+ theme(axis.text.x = element_text(angle = 90, hjust = 1))

+ theme(legend.position = "none")

+ theme_update(plot.title = element_text(hjust = 0.5))

If ggsave is slow, try:
options(bitmaptype = "cairo")

MVesuviusC

smbclient //researchshare/RESTheisen -W research -U mvc002

smbclient //igmdata/igm_roberts -W research -U mvc002

If gcc error: ml purge


# sometimes get this error:
[mvc002@r1pl-hpcf-log01 Counts_2]$ smbclient //igmdata/igm_roberts_osu -W research -U mvc002
Password for [RESEARCH\mvc002]:

MVesuviusC

vscode auto login

From:
https://stackoverflow.com/questions/66113731/how-to-save-ssh-password-to-vscode

on local machine (windows) in powershell run:
  # Change my pathway to your username #
  ssh-keygen -q -b 2048 -f /Users/mvc002/.ssh/keys/franklin_rsa -t rsa
  hit enter twice to skip entering a password

MVesuviusC

make new contents of the folder inherit group from parent directory
chmod g+s folder
https://www.redhat.com/sysadmin/suid-sgid-sticky-bit


find . -user mvc002 -group gdlessnicklab | xargs chown -v -h mvc002:gdrobertslab

MVesuviusC

git save credentials temporarily

# Store info for a day
# after you put it in once it remembers it for a day
git config --global credential.helper "cache --timeout=86400" 


usethis::create_github_token()
# Use the website to set up the github personal access token (PAT)
# Copy the PAT somewhere so you don't forget it

MVesuviusC

If you have any other choice whatsoever, just don't....


git changing history

# View file size in commits
git ls-tree -r --long c433c76cc37621189d349595adb758d54769142e

# update first commit
git rebase -i --root

MVesuviusC

conda environments

export PATH="/gpfs0/export/apps/easybuild/software/Miniconda3/4.7.10/bin:$PATH"

Package from: https://github.com/PacificBiosciences/pbbioconda

conda create -n isoseq python=2.7

eval "$(conda shell.bash hook)"

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perl install modules

cpanm [name of package]

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DNAnexus app building

source ~/virtualEnvs/dnanexus/bin/activate
dx login # login to server, choose which project to attach to
dx build # build app from the json and associated file(s)
deactivate