zshrc.numenor

#################
#
# Oh My ZSH Configuration
#
#################

ZSH=$HOME/.oh-my-zsh
# DISABLE_CORRECTION="true"
COMPLETION_WAITING_DOTS="true" # export UPDATE_ZSH_DAYS=13

# See: https://github.com/robbyrussell/oh-my-zsh/wiki/Plugins
plugins=(git ssh-agent capistrano bundler gem git-extras web-search wd python pip npm last-working-dir virtualenv)


#################
#
# Theme
#
#################


# ZSH_THEME="afowler" #beleriand
# ZSH_THEME="af-magic" # numenor
# ZSH_THEME="avit" # caladan
# ZSH_THEME="Soliah"
# ZSH_THEME="gnzh"

# ZSH_THEME="robbyrussell"
ZSH_THEME="spaceship"
# Customize spaceship THEME
SPACESHIP_USER_SHOW="never"
SPACESHIP_USER_COLOR="blue"
SPACESHIP_HOST_SHOW="always"
SPACESHIP_HOST_COLOR="yellow"
SPACESHIP_HOST_COLOR_SSH="yellow"
SPACESHIP_DIR_TRUNC=0
SPACESHIP_DIR_COLOR="blue"
SPACESHIP_JOBS_SYMBOL="(bg jobs)"
SPACESHIP_JOBS_COLOR="red"
SPACESHIP_EXIT_CODE_SHOW="true"
SPACESHIP_EXIT_CODE_PREFIX="["
SPACESHIP_EXIT_CODE_SUFFIX="]"
SPACESHIP_EXIT_CODE_SYMBOL=""
SPACESHIP_EXIT_CODE_COLOR="black"
SPACESHIP_EXEC_TIME_COLOR="black"

SPACESHIP_VENV_SYMBOL="🐍·"
SPACESHIP_VENV_COLOR="magenta"

#################
#
# Aliases and Functions
#
#################

ssh () { command ssh "$@"; eval "$("$BASE16_SHELL/profile_helper.sh")"; }

# SSH to servers
alias arrakis='ssh -XA juan@arrakis.local'
alias caladan='ssh -XA juan@caladan.local'
alias numenor='ssh -XA juan@numenor.local'
alias beleriand='ssh -XA juan@motorhome.hopto.org -p 2244'
alias motorhome='ssh -XA juan@motorhome.hopto.org -p 2244'
alias bele='ssh -XA juan@motorhome.hopto.org -p 2244'
alias solaris='mosh juan@solaris'
alias gondolin='ssh -XA juan@gondolin'
alias cluster='ssh -XA juan@cluster1'
alias cluster1='ssh -XA juan@cluster1'
alias cluster2='ssh -XA juan@cluster2'
alias uqbar='ssh juan@uqbar.local'
alias tlon='ssh juan@tlon.hopto.org'

# Common operations
alias sc='cs'
alias mv='mv -i'
alias cp='cp -iv'
alias ls='ls --color=auto --group-directories-first'
alias sl='ls --color=auto --group-directories-first'
alias l='ls --color=auto --group-directories-first'
alias ll='ls -alF --color=auto --group-directories-first'
alias la='ls -A --color=auto --group-directories-first'
alias grep='grep -i --color=auto'
alias fgrep='fgrep --color=auto'
alias egrep='egrep --color=auto'
alias ..='cs ..'
alias cs..='cs ..'
# alias tmux="tmux -2"
alias xclip="xclip -selection primary -f | xclip -selection clipboard"
alias put="xsel -p"
alias haploview='java -jar ~/software/Haploview.jar'
alias fastq-mcf='~/software/ea-utils.1.1.2-537/fastq-mcf'
alias mostusedcomms="history | awk '{CMD[\$2]++;count++;}END { for (a in CMD)print CMD[a] \" \" CMD[a]/count*100 \"% \" a;}' | grep -v \"./\" | column -c3 -s \" \" -t | sort -nr | nl |  head -n20"
alias tree='tree -F --dirsfirst --noreport'
alias tree+='tree -hF --du --dirsfirst --noreport'

# replace AWK with Ruby
alias rawk='/usr/bin/ruby2.3 -lane'
alias rawk,='/usr/bin/ruby2.3 -F, -lane'
alias rawk:='/usr/bin/ruby2.3 -F: -lane'
alias rawkt='/usr/bin/ruby2.3 -F"\t" -lane'
alias rawks='/usr/bin/ruby2.3 -F"\s+" -lane'

# Do not run feature specs by default:
alias rspec_no_feature='bundle exec rspec --exclude-pattern "spec/features/*"'
alias be='bundle exec'

# Git related aliases
push_branch() {
    branch=`git rev-parse --symbolic-full-name --abbrev-ref HEAD`
    git push $1 $branch
}
pull_branch() {
    branch=`git rev-parse --symbolic-full-name --abbrev-ref HEAD`
    git pull $1 $branch
}
autoload push_branch
autoload pull_branch

alias s='clear; git status'
alias gpo='git push origin'
alias gpom='git push origin master'
alias gpob='push_branch origin'
alias gfo='git fetch origin'
alias gfu='git fetch upstream'
alias gfot='git fetch origin --tags'
alias gfut='git fetch upstream --tags'
alias gpot='git push origin --tags'
alias gput='git push upstream --tags'
alias gpu='git push upstream'
alias gpum='git push upstream master'
alias gpub='push_branch upstream'
alias glo='git pull origin'
alias glom='git pull origin master'
alias glob='pull_branch origin'
alias glum='git pull upstream master'
alias glub='pull_branch upstream'
alias gadd='git add'

# Bioinformatics
alias gatk='java -jar /software/GenomeAnalysisTK-3.7/GenomeAnalysisTK-3.7.jar'
alias picard='java -jar /software/picard-2.18.2.jar'
alias snpeff='java -jar /software/snpEff-4.3m/snpEff.jar'
alias snpsift='java -jar /software/snpEff-4.3m/SnpSift.jar'
alias vep='/software/ensembl-tools-release-87/scripts/variant_effect_predictor/variant_effect_predictor.pl'
alias igv='/software/IGV_Linux_2.11.4/igv.sh'
alias admixture='/software/admixture_linux-1.3.0/admixture'
alias plink='/software/plink_linux_x86_64/plink'

# Tmux <3
alias tnew="tmux new-session -s"
alias tach="tmux attach-session -t"


#################
#
# Functions
#
#################

rsync_to_cluster1() {
  rsync -avzhu --progress $1 juan@cluster1:~/downloads
}
rsync_to_cluster2() {
  rsync -avzhu --progress $1 juan@cluster2:~/downloads
}

read_vcf() {
    grep -v '^##' $1 | sed 's/^#//' | column -t
}

read_vcf_no_INFO() {
    read_vcf $1 | ruby -F"\s+" -lane 'puts ($F.first(7) + $F[8..-1]).join("\t")' | column -t
}

grep_variant_from_vcf() {
    read_vcf $2 | grep -E "($1|CHROM)"
}

grep_variant_from_vcf_no_INFO() {
    read_vcf $2 | grep -E "($1|CHROM)"
}

less_vcf() {
    read_vcf $1 | less -S
}

less_vcf_no_INFO() {
    read_vcf_no_INFO $1 | column -t | less -S
}

bed_to_regions_format() {
    awk '{ print $4 "\tchr" $1 ":" $2 "-" $3}' $1
}

pswatch () {
  watch -n1 "ps aux | head -n1 && ps aux | grep '$1' | grep -v 'grep'"
}

# Doesn't work for some reason:
# https://unix.stackexchange.com/questions/27236/zsh-autocomplete-ls-command-with-directories-only
# compdef _dirs cs

cs () {
  cd $1;

  if [ $? -eq 0 ]; then  # If dir exists!
    if [ `ls | wc -l` -ge 15 ]; then
      ls --color=auto --group-directories-first;
    else
      ls -lh --color=auto --group-directories-first;
    fi
  fi
}

findhome () {
    find ~ -iname "*${1}*"
}

findhere () {
    find . -iname "*${1}"
}

backup () {
  newname=$1.`date +%Y%m%d.%H%M.bak`;
  mv $1 $newname;
  echo "-> Backed up to '$newname'";
  cp -p $newname $1;
}


#################
#
# Etc.
#
#################


if [[ -r ~/.local/lib/python2.7/site-packages/powerline/bindings/zsh/powerline.zsh ]]; then
    source ~/.local/lib/python2.7/site-packages/powerline/bindings/zsh/powerline.zsh
fi

source $ZSH/oh-my-zsh.sh

# Base16 Shell
BASE16_SHELL="$HOME/.config/base16-shell/"
[ -n "$PS1" ] && \
    [ -s "$BASE16_SHELL/profile_helper.sh" ] && \
    eval "$("$BASE16_SHELL/profile_helper.sh")"

#################
#
# PATH and variables
#
#################

export MYSQL_USER=juan
export MYSQL_PASS=glucolisis
export MYSQL_USER_REMOTE=juan
export MYSQL_PASS_REMOTE=Glucolisis!1

export PATH_TO_BCFTOOLS=/software/bcftools-1.9/bcftools
export PATH_TO_BGZIP=/software/htslib-1.9/bgzip
export PATH_TO_TABIX=/software/htslib-1.9/tabix
export PATH_TO_GATK3=/software/GenomeAnalysisTK-3.7/GenomeAnalysisTK-3.7.jar
export PATH_TO_REFERENCE_FASTA=~/Dropbox/bio/doctorado/pipeline/human_g1k_v37.fasta
export PATH_TO_JAVA=/usr/bin/java
export PATH_TO_PLINK=/software/plink_linux_x86_64/plink
export PATH_TO_RSCRIPT=/usr/bin/Rscript

export EDITOR=vim
export BROWSER=google-chrome

# export PATH=~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH
export PATH=/home/juan/anaconda3/bin:$PATH  # Anaconda
export PATH="$HOME/.rbenv/bin:$PATH"  # Rb Env

cyan=$(tput setaf 6)
export STDERRED_ESC_CODE=`echo -e "$cyan"`
export LD_PRELOAD="/home/juan/software/stderred/build/libstderred.so${LD_PRELOAD:+:$LD_PRELOAD}"

eval "$(rbenv init -)"

export PATH=$PATH:/home/juan/.rbenv/versions/2.5.1/bin

# Variant Effect Predictor breaks without this:
export PERL5LIB=/home/juan/storage/paip_resources/vep_data_87:$PERL5LIB
export PERL5LIB=/home/juan/storage/paip_resources/vep_data_90:$PERL5LIB
# export PATH=$PATH:/home/juan/storage/paip_resources/vep_data_87/htslib
# export PATH=$PATH:/home/juan/storage/paip_resources/vep_data_90/htslib
export PATH=/usr/local/texlive/2019/bin/x86_64-linux:$PATH

export CLUSTER="juan@cluster1"

eval "$(dircolors ~/.dircolors)";