[ncl-talk] activate the NCL environment from within a shell script

[Sam McClatchie]

Colleagues

[I am using Ubuntu 18.04]

I want to call an NCL script from a bash shell script. Normally I would 
just activate the environment from the command line:

(base) smcc at Jaguar:~$ conda activate ncl_stable
(ncl_stable) smcc at Jaguar:~$

and then run the shell script in the terminal:

./download_latest_GHRSST_data_from_ERDdap.sh

This works fine.

The problem is that I want to automate by using a shell script called in 
a cron job. I want to incorporate this NCL script in a cron job 
containing other calls to R, so being able to activate the NCL 
environment from within a shell script would be helpful. I suspect 
others have done something similar, so I'd appreciate your guidance.

### details follow #########################

When I try to activate the NCL environment from a bash shell script using:

/home/smcc/anaconda3/bin/conda activate ncl_stable

in the shell script, the following error is returned:

(base) 
smcc at Jaguar:/mnt/data/dynamic_data/projects/projects2020/recreational_fishing_GHRSST/shell$ 
./download_latest_GHRSST_data_from_ERDdap.sh

Error message start ---------------------------

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'.

./download_latest_GHRSST_data_from_ERDdap.sh: line 19: ncl: command not 
found
(base) 
smcc at Jaguar:/mnt/data/dynamic_data/projects/projects2020/recreational_fishing_GHRSST/shell$ 

Error message end --------------------------------------------

Running conda init bash before calling the shell script does not fix the 
problem.

(ncl_stable) 
smcc at Jaguar:/mnt/data/dynamic_data/projects/projects2020/recreational_fishing_GHRSST/shell$ 
conda init bash
no change     /home/smcc/anaconda3/condabin/conda
no change     /home/smcc/anaconda3/bin/conda
no change     /home/smcc/anaconda3/bin/conda-env
no change     /home/smcc/anaconda3/bin/activate
no change     /home/smcc/anaconda3/bin/deactivate
no change     /home/smcc/anaconda3/etc/profile.d/conda.sh
no change     /home/smcc/anaconda3/etc/fish/conf.d/conda.fish
no change     /home/smcc/anaconda3/shell/condabin/Conda.psm1
no change /home/smcc/anaconda3/shell/condabin/conda-hook.ps1
no change /home/smcc/anaconda3/lib/python3.7/site-packages/xontrib/conda.xsh
no change     /home/smcc/anaconda3/etc/profile.d/conda.csh
no change     /home/smcc/.bashrc
No action taken.

Another recommendation was to prepend a line to the bash script:

eval "$(command conda 'shell.bash' 'hook' 2> /dev/null)"

but this doesn't seem to work when I call the shell script from cron.

My cron file is just one line calling the shell script to run interactively:

0 12 * * * bash -i 
/mnt/data/dynamic_data/projects/projects2020/recreational_fishing_GHRSST/shell/download_latest_GHRSST_data_from_ERDdap.sh

and here is my shell script:

start shell script ------------------------------

eval "$(command conda 'shell.bash' 'hook' 2> /dev/null)"
#!/bin/bash
## download_latest_GHRSST_data_from_ERDdap.sh
# NOTE: for this script to work, call the script in cron using:
# "bash -i ./download_latest_GHRSST_data_from_ERDdap.sh"
# to run the script in interactive mode so the .bashrc file is sourced
# Otherwise conda activate will not work

# Use crontab -e to edit the cron file
# (see https://linux4one.com/how-to-set-cron-jobs-on-ubuntu-18-04/)
# use cronitor to troubleshoot cron file
# (see https://cronitor.io/cron-reference/cron-troubleshooting-guide).
# Try $ cronitor select to test run

########################################
# download the latest GHRSST data from erddap
########################################
  # Rscript 
"/mnt/data/dynamic_data/projects/projects2020/recreational_fishing_GHRSST/R/download_GHRSST_MUR-JPL-L4-GLOB-v4.1_daily.R"

########################################
# plot GHRSST data
########################################
# activate the ncl environment
conda activate ncl_stable

ncl 
/mnt/data/dynamic_data/projects/projects2020/recreational_fishing_GHRSST/ncl/plot_daily_GHRSST-MUR-JPL-L4-GLOB-v4_1_around_New_Zealand.ncl

end shell script -------------------------------

Best fishes

Sam

-- 
email signature Sam McClatchie (fisheries oceanographer)
& Elena Turin (accounting & auditing)
FishOcean Enterprises www.fishocean.info <http://www.fishocean.info>
38 Upland Rd, Huia, Auckland 0604, New Zealand
cell: 027 752 8495


"The time has come", the tui said,
"to talk of many things:
Of songs - and ferns - and flowering flax,
of pukekos and dreams ..."

(not Lewis Carroll)
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