local_R.md

To install R locally, follow the steps below.

# Set your working directory
work_dir=
[ -z "$work_dir" ] && echo "Set work_dir!" && return 1
[ ! -d $work_dir ] && mkdir $work_dir

# Make github/app directories
git_dir=$work_dir/github
[ ! -d $git_dir ] && mkdir $git_dir

apps_dir=$work_dir/apps
[ ! -d $apps_dir ] && mkdir $apps_dir

# Clone/Pull repo
cd $git_dir
[ ! -d baSHic ] && git clone https://github.com/pllittle/baSHic.git
[ -d baSHic ] && cd baSHic && git pull

# Source environment script
. $git_dir/baSHic/scripts/getEnv.sh
[ ! $? -eq 0 ] && echo "Some error at getEnv" && return 1
	# If there's an error here, getEnv.sh needs to be updated

# Source R and dependency function scripts
. $git_dir/baSHic/scripts/install_R.sh

# Install R
install_R -a $apps_dir

If there are errors, follow the output or drop me an issue.

Common Errors