.bashrc file conda

.bash_profile

# in order to load the .bashrc by default, it must be in the `.bash_profile`
# https://askubuntu.com/questions/161249/bashrc-not-executed-when-opening-new-terminal

# include .bashrc if it exists
if [ -f "$HOME/.bashrc" ]; then
    . "$HOME/.bashrc"
fi

.bashrc

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/bit/ashar/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/bit/ashar/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/home/bit/ashar/anaconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/bit/ashar/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

export PATH=~/anaconda3/bin:$HOME/curl/bin:$PATH
export R_USER=/home/bit/ashar/R
export R_LIBS="/home/bit/ashar/R/x86_64-pc-linux-gnu-library/3.6"

b-it setup.Rmd

# example b-it servers anaconda installation

## purpose
recipe to run anaconda3 on the b-it server. there are two cases

### case 1
check if anaconda is installed.
- go to your home folder, look for an anconda folder, go into that folder and check the content

if it is installed, but you can't start it via typing `conda` in the terminal, then probably the 
executable is not in the path and some initialization is missing,
then create/adapt the `.bashrc` in your home folder accordingly.
in addition create/adapt the `.bash_profile` in your home folder accordingly.

after you adapted/created the `.bashrc` and the `.bash_profile`, exit from terminal and reconnect.
if everything went fine, conda will be started automatically in the `base` env  when connecting to the server.

### case 2
if anaconda isn't installed, follow the _## step by step installation_ procedure below.

## step by step installation

first, get the proper/desired version from https://www.anaconda.com/distribution/. 
for the b-it case it’s https://repo.anaconda.com/archive/Anaconda3-2019.10-Linux-x86_64.sh 
login to b-it server and download the file, eg `wget https://repo.anaconda.com/archive/Anaconda3-2019.10-Linux-x86_64.sh`

open a screen so that the installation can run in the background: `screen -R inst_anaconda`
start the setup, in this case: `bash Anaconda3-2019.10-Linux-x86_64.sh` and follow the setup instructions.
this may take a while!
then detach from screen using `CTRL + A + D`.
to re-attach to the screen later from the console, do `screen -r inst_anaconda`
if the installation has finished, exit from the attached screen with `exit + ENTER`

## check the installation
type `conda`. if this doesn't work, then create/update the `.bashrc` and `.bash_profile` file as described before in _### case 1_ section.

finally, enter `conda update --all --yes` to update anaconda.

# references
see the conda cheat sheet https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf

using "screens" https://wiki.ubuntuusers.de/Screen/

https://mas-dse.github.io/startup/anaconda-ubuntu-install/