jhpce_mac_setup_log.txt

Hi!

Here’s the recording from my session today with Sang Ho, Kristen and Abby. 

Here are the links and content for several config files I gave Sang Ho throughout the session:

R https://cran.r-project.org/
RStudio https://rstudio.com/products/rstudio/download/#download
JHPCE register: https://jhpce.jhu.edu/register/user/
JHPCE ssh keys: https://jhpce.jhu.edu/knowledge-base/authentication/ssh-key-setup/

Laptop ~/.ssh/config:

touch config
open config

Host j jhpce
    User YOUR_USERNAME
    Hostname jhpce01.jhsph.edu
    ForwardX11 yes
    ForwardX11Trusted yes

Cyberduck https://cyberduck.io/
JHPCE ~/.Rprofile (can also be applied to your laptop):

## Change colors
# Source https://github.com/jalvesaq/colorout
if(Sys.getenv('TERM') %in% c("term", "xterm-256color", "cygwin", "screen") & interactive()) {
	installed <- require("colorout")
	if(!installed) {
		cat('remotes::install_github("jalvesaq/colorout")\n')
	}
	rm(installed)
}

JHPCE ~/.inputrc (can also be applied to your laptop):

#Page up/page down
"\e[B": history-search-forward
"\e[A": history-search-backward
$include /etc/inputrc

JHPCE ~/.bashrc (not the same as laptop!!)

# .bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi
# User specific aliases and functions
# Auto-complete command from history
# http://lindesk.com/2009/04/customize-terminal-configuration-setting-bash-cli-power-user/
export INPUTRC=~/.inputrc
# http://www.biostat.jhsph.edu/~afisher/ComputingClub/webfiles/KasperHansenPres/IntermediateUnix.pdf
# https://unix.stackexchange.com/questions/48713/how-can-i-remove-duplicates-in-my-bash-history-preserving-order
export HISTCONTROL=ignoreboth:erasedups
export HISTSIZE=20000
shopt -s histappend
shopt -s cmdhist
# http://superuser.com/questions/384769/alias-rm-rm-i-considered-harmful
alias rmi='rm -i'
# Change command prompt
# http://www.cyberciti.biz/tips/howto-linux-unix-bash-shell-setup-prompt.html
# http://www.cyberciti.biz/faq/bash-shell-change-the-color-of-my-shell-prompt-under-linux-or-unix/
# https://bbs.archlinux.org/viewtopic.php?id=48910
# previous in enigma2: "[\u@\h \W]\$ "
# previously in mac: "\h:\W \u\$ "
export PS1="\[\e[0;33m\]\A \W \$ \[\e[m\]"
# Main working directory
alias labold="cd /dcl01/lieber/ajaffe/lab"
# colors
# http://norbauer.com/notebooks/code/notes/ls-colors-and-terminal-app
# used BSD pattern ExGxFxDxBxEgEdxbxgxhxd on http://geoff.greer.fm/lscolors/
# that tool does not specify the colors, which I did by looking manually at
# http://blog.twistedcode.org/2008/04/lscolors-explained.html
# and the norbauer.com site previously mentioned
alias ls="ls --color=auto"
#export LS_COLORS="di=1;34;40:ln=1;36;40:so=1;35;40:pi=1;93;40:ex=1;31;40:bd=1;34;46:cd=1;34;43:su=0;41:sg=0;46:tw=0;47:ow=0;43"
## After switching to RStudio:
# https://askubuntu.com/questions/466198/how-do-i-change-the-color-for-directories-with-ls-in-the-console
export LS_COLORS="di=0;32:ln=0;36:so=0;35:pi=0;93:ex=0;31:bd=0;34;46:cd=0;34;43:su=0;41:sg=0;46:tw=0;47:ow=0;43:fi=0;33"
## Load the git module by default when qrsh/qsub
## thanks to Jiong Yang
if [[ $HOSTNAME == compute-* ]]; then
    echo "Adding LIBD modules"
    module use /jhpce/shared/jhpce/modulefiles/libd
    echo "Loading git"
    module load git
    module load git-status-size/github
    module load git-lfs/2.8.0
    module load rmate/1.5.9
    module load conda_R/3.6.x
fi
## To deal with running nextflow without requesting much more memory
## https://jhpce.jhu.edu/question/why-do-i-get-memory-errors-when-running-java/
export _JAVA_OPTIONS="-Xms5g -Xmx6g"

JHPCE ~/.bashrc alias for spatial 10x (not for everyone!):

## Shortcut alias
alias spatial="cd /dcl02/lieber/ajaffe/SpatialTranscriptomics/HumanPilot"

Example reproducibility code we saved in JHPCE at ~/reproducibility.R:

library('sessioninfo')

## Wait for 60 seconds (did this with Kristen, not on the video)
Sys.sleep(60)

## Reproducibility information
print('Reproducibility information:')
Sys.time()
proc.time()
options(width = 120)
session_info()

sgejobs package website http://research.libd.org/sgejobs/index.html
JHPCE default config ~/.sge_request:
# Set a default maximum file size that an SGE job can create
-l h_fsize=100G

# Define my email
-M YOUR_EMAIL@gmail.com
# To get an email on a job use -m e