RaymondSHANG

How to have specific .gitignore for each git branch

Objective

My objective is to have some production files ignored on specific branches. Git doesn't allow to do it.

Solution

My solution is to make a general .gitignore file and add .gitignore.branch_name files for the branches I want to add specific file exclusion. I'll use post-checkout hook to copy those .gitignore.branch_name in place of .git/info/exclude each time I go to the branch with git checkout branch_name.

RaymondSHANG

"My First WDL" Template

task name {
  String in
  command {
    echo '${in}'
  }
  output {
 String out = read_string(stdout())

RaymondSHANG

How to submit R code to a Portable Batch System (PBS) managed High Performance Computing (HPC) Facility (e.g. QUT's HPC Facility 'Lyra').

You will need:

1. An account with the relevant HPC facility (QUT staff and HDR students can request access to the QUT facility here),
2. the R Script (.R file) you want to run,
3. a Job Script (.sub file) that tells Lyra how to run your R script and,
4. a file containing any data your R Script needs to run.

Note: These instructions work on a system running Debian (GNU + Linux) with the Gnome Desktop Environment.

RaymondSHANG

Technical details for https://stackoverflow.com/a/44169445/6730571

Details of investigation:

On a base system, /usr/bin/java is a symlink that points to /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/java, which is an Apple wrapper tool that locates and executes the actual java.

(Do not touch anything in those 2 system directories. It should actually be impossible due to "System Integrity Protection" anyway.)

If you don't have Java installed, attempting to execute java will open a dialog that invites you to install it.

RaymondSHANG

# restore_packages.R
#
# installs each package from the stored list of packages
# source: http://hlplab.wordpress.com/2012/06/01/transferring-installed-packages-between-different-installations-of-r/

load("~/installed_packages.rda")

for (count in 1:length(installedpackages)) {
    install.packages(installedpackages[count])
}