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bash_aliases
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# enable color support of ls and also add handy aliases
if [ -x /usr/bin/dircolors ]; then
test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
alias ls='ls --color=auto'
alias dir='dir --color=auto'
alias vdir='vdir --color=auto'
alias grep='grep --color=auto'
alias fgrep='fgrep --color=auto'
alias egrep='egrep --color=auto'
fi
alias ll='ls -alF'
alias la='ls -A'
alias l='ls -CF'
alias rm='rm -i'
alias del="$HOME/src/move_to_trash.sh"
## Modify the R version folders (in src/svn) after every release
## Note. These folders correspond to ./buildr.sh
alias Rold="R_LIBS_USER=$HOME/R/bioc-oldrel $HOME/src/svn/r-4-0/R/bin/R --no-save --no-restore-data --no-environ"
alias Rrel="R_LIBS_USER=$HOME/R/bioc-release $HOME/src/svn/r-4-1/R/bin/R --no-save --no-restore-data --no-environ"
alias Rdev="R_LIBS_USER=$HOME/R/bioc-devel $HOME/src/svn/r-4-2/R/bin/R --no-save --no-restore-data"
alias rstudev="RSTUDIO_WHICH_R=$HOME/src/svn/r-devel/R/bin/R R_LIBS_USER=$HOME/R/bioc-devel rstudio --no-save --no-restore-data --no-environ"
alias rsturel="RSTUDIO_WHICH_R=$HOME/src/svn/r-release/R/bin/R R_LIBS_USER=$HOME/R/bioc-release rstudio --no-save --no-restore-data --no-environ"
## If you need independent R libraries for testing
## alias r40="R_LIBS_USER=$HOME/R/r-4-0 $HOME/src/svn/r-4-0/R/bin/R --no-save --no-restore-data --no-environ"
## alias r41="R_LIBS_USER=$HOME/R/r-4-1 $HOME/src/svn/r-4-1/R/bin/R --no-save --no-restore-data --no-environ"
## alias r42="R_LIBS_USER=$HOME/R/r-4-2 $HOME/src/svn/r-4-2/R/bin/R --no-save --no-restore-data --no-environ"
## alias devel="R_LIBS_USER=$HOME/R/r-devel $HOME/src/svn/r-devel/R/bin/R --no-save --no-restore-data --no-environ"
alias installr='Rrel CMD INSTALL --no-test-load --no-staged-install'
alias installd='Rdev CMD INSTALL --no-test-load --no-staged-install'
alias buildr='Rrel CMD build --no-build-vignettes'
alias buildd='Rdev CMD build --no-build-vignettes'
alias checkr='time Rrel CMD check --no-vignettes --no-manual'
alias checkd='time Rdev CMD check --no-vignettes --no-manual'
alias bioccheck='Rdev -e "BiocCheck::BiocCheck()"'
## For vim users who need different versions of R
## alias vimo='R_LIBS_USER=$HOME/R/bioc-oldrel/ RLOC=$HOME/src/svn/r-oldrel/R/bin vim'
## alias vimr='R_LIBS_USER=$HOME/R/bioc-release/ RLOC=$HOME/src/svn/r-release/R/bin vim'
## alias vimd='R_LIBS_USER=$HOME/R/bioc-devel/ RLOC=$HOME/src/svn/r-devel/R/bin vim'
alias locate='locate -i'
alias sudo='sudo '
alias tmux="TERM=screen-256color-bce tmux"
alias fullpath='readlink -f'
alias bump="$HOME/scripts/version_bump.sh"
alias rm='rm -i'
if [ -x /usr/bin/subversion ]; then
alias svnvimdiff="svn diff -r PREV | view -"
fi
# The next line updates PATH for the Google Cloud SDK.
if [ -f $HOME/src/google-cloud-sdk/path.bash.inc ]; then
source $HOME/src/google-cloud-sdk/path.bash.inc
fi
# The next line enables shell command completion for gcloud.
if [ -f $HOME/src/google-cloud-sdk/completion.bash.inc ]; then
source $HOME/src/google-cloud-sdk/completion.bash.inc
fi
alias gitall="find . -maxdepth 1 -mindepth 1 -type d -exec sh -c '(echo {} && cd {} && git status -s && echo)' \;"
alias git.addnw="git diff -U0 -w --no-color --src-prefix=a/ --dst-prefix=b/ | git apply --cached --ignore-whitespace --unidiff-zero -"
alias scrub='find . -maxdepth 1 -type f -name "*.tar.gz" -exec rm {} \; && find . -maxdepth 1 -type d -name "*.Rcheck" -exec rm -rf {} \; && find . -maxdepth 1 -type d -name "*.BiocCheck" -exec rm -rf {} \;'