# ~/.bashrc: executed by bash(1) for non-login shells.
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples

# If not running interactively, don't do anything
case $- in
    *i*) ;;
      *) return;;
esac

# don't put duplicate lines or lines starting with space in the history.
# See bash(1) for more options
HISTCONTROL=ignoreboth

# append to the history file, don't overwrite it
shopt -s histappend

# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
#
# HISTSIZE description
# The maximum number of commands to remember on the history list.
# If the value is 0, commands are not saved** in the history list. 
# Numeric values less than zero result in every command being saved on the history list (there is no limit). 
# HISTSIZE=1000
HISTSIZE=-1
#
# HISTFILESIZE description
# Non-numeric values and numeric values less than zero inhibit truncation.
# HISTFILESIZE=2000
HISTFILESIZE=-1

# check the window size after each command and, if necessary,
# update the values of LINES and COLUMNS.
shopt -s checkwinsize

# If set, the pattern "**" used in a pathname expansion context will
# match all files and zero or more directories and subdirectories.
#shopt -s globstar

# make less more friendly for non-text input files, see lesspipe(1)
[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"

# set variable identifying the chroot you work in (used in the prompt below)
if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
    debian_chroot=$(cat /etc/debian_chroot)
fi

# set a fancy prompt (non-color, unless we know we "want" color)
case "$TERM" in
    xterm-color) color_prompt=yes;;
esac

# uncomment for a colored prompt, if the terminal has the capability; turned
# off by default to not distract the user: the focus in a terminal window
# should be on the output of commands, not on the prompt
#force_color_prompt=yes

if [ -n "$force_color_prompt" ]; then
    if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
	# We have color support; assume it's compliant with Ecma-48
	# (ISO/IEC-6429). (Lack of such support is extremely rare, and such
	# a case would tend to support setf rather than setaf.)
	color_prompt=yes
    else
	color_prompt=
    fi
fi

if [ "$color_prompt" = yes ]; then
    PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
else
    PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
fi
unset color_prompt force_color_prompt

# If this is an xterm set the title to user@host:dir
case "$TERM" in
xterm*|rxvt*)
    PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
    ;;
*)
    ;;
esac

# 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

# some more ls aliases
alias ll='ls -alF'
alias la='ls -A'
alias l='ls -CF'

# Add an "alert" alias for long running commands.  Use like so:
#   sleep 10; alert
alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal || echo error)" "$(history|tail -n1|sed -e '\''s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\'')"'

# Alias definitions.
# You may want to put all your additions into a separate file like
# ~/.bash_aliases, instead of adding them here directly.
# See /usr/share/doc/bash-doc/examples in the bash-doc package.

if [ -f ~/.bash_aliases ]; then
    . ~/.bash_aliases
fi

# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if ! shopt -oq posix; then
  if [ -f /usr/share/bash-completion/bash_completion ]; then
    . /usr/share/bash-completion/bash_completion
  elif [ -f /etc/bash_completion ]; then
    . /etc/bash_completion
  fi
fi

# Path to BWA aligner
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/bwa-0.7.10

# Path to samtools
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/samtools-1.2
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/samtools-1.2

# Path to bcftools
# export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/bcftools-1.2
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/bcftools-1.4

# Path to HTSlib
# export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/htslib-1.2.1
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/htslib-1.4

# Path to picard-tools
# export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/picard-tools-1.119
# export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/picard-tools-1.119
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/picard-2.9.0


# Path to FastQC:
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/FastQC/fastqc

# Path to GATK:
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/GATK-3.3-0

# path to VCFtools:
# export PERL5LIB=/home/jlorsal/Escritorio/drago/apps/vcftools_0.1.12b/perl
# export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/vcftools_0.1.12b/bin
# export PERL5LIB=/home/jlorsal/Desktop/drago/apps/vcftools_0.1.12b/perl
# export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/vcftools_0.1.12b/bin
export PERL5LIB=/home/jlorsal/Desktop/drago/apps/vcftools_0.1.14-31/perl
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/vcftools_0.1.14-31/bin

# path to BEDtools:
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/bedtools-2.17.0
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/bedtools2

# path to PLINK:
# export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/plink-1.07-x86_64
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/plink-1.07-x86_64

# path to LASER:
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/LASER_2.01

# path to HAPLOVIEW:
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/haploview

# path to HAPLOVIEW:
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/fcgene-1.0.7

# path to EIGENSOFT "master":
export PATH=$PATH:/opt/EIG-6.1.4/bin

# path to IGV:
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/IGV_2.3.34

# path to ANNOVAR:
#export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/annovar
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/annovar
#export PATH=$PATH:/media/jlorsal/drago/annovar2016

# path to somatypus:
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/somatypus/src

# path to somatypus:
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/somatypus/src

# path to platypus:
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/Platypus_0.8.1

# path to sambamba:
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/sambamba

# path to permanently add the compilers to your system’s path. See https://solarianprogrammer.com/2014/08/26/building-gcc-on-ubuntu-linux/
export PATH=$PATH:/usr/gcc_4_9/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/gcc_4_9/lib:/usr/gcc_4_9/lib64

# path to locate python3 if necessary:
export PATH=$PATH:/usr/local/lib
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib

# path to ProABEL:
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/probabel-0.5.0

# path to EPACTS:
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/EPACTS-3.2.6

# path to VarSeq:VarSeq
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/VarSeq

# path to qualimap
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/qualimap_v2.1

# path to MetaSoft
# export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/metasoft
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/metasoft

# path to snpEff
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/snpEff

# path to METASOFT
export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/metasoft

# path to matlab
export PATH=$PATH:/media/jlorsal/drago/matlab/bin

# path to Affimetrix APT tools
#export PATH=$PATH:/home/jlorsal/Escritorio/AffyPipe/AFFYTOOLS/apt-1.19.0-x86_64-intel-linux/bin
#export PATH=$PATH:/home/jlorsal/Escritorio/drago/apps/AffyPipe/AFFYTOOLS/apt-1.16.0-x86_64-intel-linux/bin
export PATH=$PATH:/media/jlorsal/drago/Affy_fnl/AFFYTOOLS/apt-1.19.0-x86_64-intel-linux/bin

# path to DosageConverter (Abecasis Lab)
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/DosageConvertor
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/DosageConvertor/bin

# path to agilentreadtrimmer
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/AgilentReadTrimmer

# path to seqtk
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/seqtk

# path to exomeCQA and genIndex
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/ExomeCQA

# path to mixPainter
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/mixPainter

# path to chromoPainter
export PATH=$PATH:/opt/chromopainter-0.0.4

# path to ALDER
export PATH=$PATH:/opt/alder

# path to mosdepth
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/mosdepth

# path to ELAI
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/elai-lin

# path to PSMC
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/psmc
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/psmc/utils

# path to BaseSpace-CLI (Command Line Interface)
export PATH=$PATH:/home/jlorsal/bin/bs
export PATH=$PATH:/home/jlorsal/bin/bs-cp

# path to SHAPEIT
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/shapeit.v2.904.3.10.0-693.11.6.el7.x86_64/bin

# path to selection_stats
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/selection_stats
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/selection_stats/src

# path to ANGSD
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/angsd
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/angsd/misc

# path to ms Hudson
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/ms

# path to STRELKA
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/strelka-2.9.2.centos6_x86_64/bin

# path to MANTA
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/manta-1.4.0.centos6_x86_64/bin

# path to ILMN PISCES
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/Pisces_5.2.7.47

# path to iSAFE
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/iSAFE/src

# path to CORTEX analyse-variants bioinfo-perl
export PERL5LIB=/home/jlorsal/Desktop/drago/apps/CORTEX_release_v1.0.5.21/scripts/analyse_variants/bioinf-perl/lib
export PERL5LIB=/home/jlorsal/Desktop/drago/apps/CORTEX_release_v1.0.5.21/scripts/calling

# path to interop de IMLN BaseSpace para usar como módulo de MultiQC
# Con summary obtenemos el "summary" tab de ILMN SAV en formato CSV para poder abrir con MultiQC
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/interop/src/apps

# path to ELAI
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/elai

# path to fastq-join
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/fastq-join

# path to RAiSD
export PATH=$PATH:/home/jlorsal/Desktop/drago/apps/RAiSD/raisd-master/bin/release

# set PATH so that it includes user's private bin if it exists
if [ -d "$HOME/.local/bin" ] ; then
    PATH="${PATH+$PATH:}$HOME/.local/bin"
fi

# NO OLViDAR HACER "source ~/.bashrc" al terminar de editar este fichero


#THIS MUST BE AT THE END OF THE FILE FOR SDKMAN TO WORK!!!
export SDKMAN_DIR="/home/jlorsal/.sdkman"
[[ -s "/home/jlorsal/.sdkman/bin/sdkman-init.sh" ]] && source "/home/jlorsal/.sdkman/bin/sdkman-init.sh"

# added by Miniconda3 installer
export PATH="/home/jlorsal/Desktop/drago/apps/miniconda3/bin:$PATH"