Questions[anaconda](ubuntu)

I am trying to write a script with the name myscrpt.sh, so when I run it it automatically creates a virtual env and activate it using conda. My conda version is 4.7.1.

This is what I have at the beginning of my myscrpt.sh:

#!/bin/bash
conda create --name myenv1
conda activate myenv1

creating the environment is not a problem, however I get the error:

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

I don't get this error if I run conda activate myenv1 directly in my terminal.

So far I have taken several measures such as using conda init <SHELL_NAME> which did not help at all. Then I added the following in my bashrc

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

which also didnt work. Next and according to this link changed the path in the PATH line to:

. /opt/conda/etc/profile.d/conda.sh
conda activate base

This one was written for conda 4.4, but I was hoping wouold help me.

Then I tried conda run instead of conda activate, but this also did not help.

So any ideas how can I get this working? :)

UPDATE1: Now I use source ./myscript.sh, and activating works fine, but it gets to errors in conda install.

I'm getting this while installing anaconda on ubuntu 19.04

When I try to get the manpages with man it seems to display nothing and behaves as though I just pressed enter

~$ man ls
~$ man man

I have tried solutions from these pages to no avail question1 question2. This last question matches my condition exactly but the fixes doesn't seem to work. Although info seems to work.

Here are some additional information:

~$ man --version
man 2.7.6.1

~$ type -p man
/usr/bin/man

~$ type -t man
file

~$ manpath
/home/abhilash/anaconda3/man:/usr/local/man:/usr/local/share/man:/usr/share/man:/usr/lib/jvm/java-8-oracle/man

~$ uname -a
Linux abhilash-ThinkPad-T440 4.13.0-38-generic #43-Ubuntu SMP Wed Mar 14 15:20:44 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

UPDATE

~$ type -a man
man is /usr/bin/man

~$ env | grep 'PAGER\|^MAN'
~$ 

UPDATE 2

~$ ls -1 /usr/share/man/man1 | wc -l
2145

~$ ls -l "$(type -p pager)"
lrwxrwxrwx 1 abhilash abhilash 18 Apr 16 18:43 /home/abhilash/anaconda3/bin/pager -> ../lib/R/bin/pager

~$ ls -l "$(readlink "$(type -p pager)")"
ls: cannot access '../lib/R/bin/pager': No such file or directory

I'm wondering why I have (base) on the left of my terminal prompt.

If I run source ~/.profile in the terminal, it disappears.

If I close that terminal and reopen a new terminal, (base) is there again.

I'd like to know what it is.

Here's the content of my .profile (excluding standard $path stuff and other personalized things):

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

Here's the content of my .bashrc

# 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=1000
HISTFILESIZE=2000

# 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|*-256color) 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

# colored GCC warnings and errors
#export GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'

# 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

# added by Anaconda3 installer
#export PATH="/home/jim/anaconda3/bin:$PATH"
. /home/jim/anaconda3/etc/profile.d/conda.sh
conda activate

I have used the guide from similar question (How can I create launchers on my desktop?)

but nothing works when it comes to Ananconda3 shortcut.

Here is my desktop file for anaconda:

[Desktop Entry]
Version=1.0
Type=Application
Name=Anaconda-Navigator
GenericName=Anaconda
Exec=bash -c anaconda-navigator
Icon=/home/paygilant/anaconda3/lib/python3.6/site-packages/anaconda_navigator/s$
Terminal=false
StartupNotify=true
MimeType=text/x-python;

I have succeeded the image part, but can't actually launch it. There is an icon on my desktop and I have put in the command bash -c anaconda-navigator.

Please help me identify what am I missing?