@@ -1,14 +1,15 @@

 # Title: .bash_profile

 # Author: Frédéric CHEVALIER <f15.chevalier@gmail.com>

-# Version: 2.3

+# Version: 3.0

 # Created in: 2012-05-25

-# Modified in: 2019-03-10

+# Modified in: 2020-03-01

 #==========#

 # Versions #

 #==========#

+# v3.0 - 2020-03-01: Linuxbrew added / Miniconda added / some Python env variables removed / R env variables removed / PATH setup improved / misc updates

 # v2.3 - 2019-03-10: alias updated / R hack for medusa2 added / no ssh key usage or storage for heron

 # v2.2 - 2017-04-23: server name updated / SSH connection through screen improved / welcome message improved

 # v2.1 - 2016-07-25: bug about space corrected / exit if not interactive (due to Grid Engine)

@@ -37,10 +38,7 @@

 [[ -z "$PS1" ]] && return

 # Load bashrc file

-if [[ -f ~/.bashrc ]]

-then

-	source ~/.bashrc

-fi

+[[ -f ~/.bashrc ]] && source ~/.bashrc

@@ -89,14 +87,14 @@ bind 'set show-all-if-unmodified off'

 #-------#

 # Path variable

-export PATH=$HOME/local/bin:$HOME/local/share:$HOME/local/usr/local/bin:$PATH     # Personal path

+[[ $SHLVL -eq 1 ]] && export PATH=$HOME/local/bin:$HOME/local/share:$HOME/local/usr/local/bin:$PATH     # Personal path

+

+# Linuxbrew

+[[ $SHLVL -eq 1 && -d "$HOME/.linuxbrew" ]] && eval $("$HOME/.linuxbrew/bin/brew" shellenv)

 # Use of personal /lib* if recent OS

-if [[ $(lsb_release -r 2> /dev/null | cut -f 2) > 6.4 || $(grep -i "version_id" /etc/os-release 2> /dev/null | cut -d "\"" -f 2) > 6.4 ]]

-then

-    # Location of bamtools lib (source: http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/bamtools.htm)

-    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/local/lib:$HOME/local/lib64"

-fi

+# Location of bamtools lib (source: http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/bamtools.htm)

+export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/local/lib:$HOME/local/lib64"

 # Special paths for perseus, medusa and nodes

 if [[ $HOSTNAME =~ perseus* || $HOSTNAME =~ medusa* || $HOSTNAME =~ compute.* ]]

@@ -114,10 +112,7 @@ fi

 export PERL5LIB=~/local/lib/perl5/site_perl/5.18.2/x86_64-linux/auto:~/local/lib/perl5/5.18.2:~/local/lib/perl5/site_perl:~/local/lib/perl5/site_perl/5.18.2:~/local/lib/perl5/site_perl/5.18.2/x86_64-linux:~/local/lib/perl5/5.18.2/x86_64-linux:/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi:/usr/lib/perl5/site_perl/5.8.8:/usr/lib/perl5/site_perl:/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi:/usr/lib/perl5/vendor_perl/5.8.8:/usr/lib/perl5/vendor_perl:/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi:/usr/lib/perl5/5.8.8

 # Python

-python_version=$(python --version 2>&1 | cut -d " " -f2 | cut -d "." -f -2)

-export PYTHONPATH=$HOME/local/lib/python${python_version}/site-packages

 export PYTHONIOENCODING=utf-8

-unset python_version

 #----------#

@@ -133,20 +128,12 @@ export CONSED_HOME=~/local/bin/consed.d

 # Vim

 export VIMHOME=$HOME/.vim

-# R

-R_version=$(R --version | head -1 | cut -d " " -f 3)

-export R_LIBS_HOME="$HOME/.R-libs"

-

-if [[ ! -d "${R_LIBS_HOME}/${R_version}" ]]

-then

-    mkdir "${R_LIBS_HOME}/${R_version}"

-fi

-

-export R_LIBS="${R_LIBS_HOME}/${R_version}"

-

+# Miniconda

+[[ -d "$HOME/.miniconda3" ]] && source "$HOME/.miniconda3/etc/profile.d/conda.sh"

+[[ -n $CONDA_DEFAULT_ENV ]]  && conda activate $CONDA_DEFAULT_ENV

 # OPAM completion

-source $HOME/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true

+[[ $SHLVL -eq 1 ]] && source $HOME/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true

 # Git completion

 [[ -s "/etc/bash_completion.d/git" ]] && source /etc/bash_completion.d/git

@@ -154,6 +141,9 @@ source $HOME/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true

 # Biom completion

 [[ $(which biom &> /dev/null ; echo $?) == 0 ]] && eval "$(_BIOM_COMPLETE=source biom)"

+# Linuxbrew completion

+[[ -s "$HOME/.linuxbrew/etc/bash_completion.d/brew" ]] && source "$HOME/.linuxbrew/etc/bash_completion.d/brew"

+

 # SSH environment setup

 SSH_KEY_LIST="$HOME/.ssh/key_list"  # File with full path of keys (one per line) to load with start_agent