clean-up

scripts/make_demonstrator.sh

-#!/bin/bash
-
-# This script fully installs the Nyx tagging UI together with MaggotUBA
-# on a newly created user account.
-# Some steps are not expected to work from any workstation:
-# sample data and restricted-access code are moved from a specific location.
-# Additional steps include making a `larvatagger` command to launch the
-# Nyx tagging UI, with specific options for our beloved alpha-testers.
-
-if ! [ -x ~/.local/bin/julia ]; then
-# install JILL with pip
-python3 -m pip install jill
-# install Julia with JILL
-python3 -m jill install --confirm
-fi
-# make the `julia` command available on the commandline
-export PATH=~/.local/bin:$PATH
-# get LarvaTagger.jl source
-# (the dev branch is used here for pre-release testing purposes)
-git clone https://gitlab.pasteur.fr/nyx/larvatagger.jl LarvaTagger -b dev
-cd LarvaTagger
-# install LarvaTagger.jl with Pkg
-julia --project=. -e 'using Pkg; Pkg.instantiate()'
-if ! [ -x ~/.local/bin/larvatagger.jl ]; then
-pushd ~/.local/bin
-ln -s ~/LarvaTagger/scripts/larvatagger.jl .
-popd
-fi
-# get MaggotUBA source and trained models - open-source part
-git clone https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA -b 20220418
-cd MaggotUBA
-# install Poetry with pip
-python3 -m pip install poetry
-# install MaggotUBA with Poetry; this step requires access to a private repo;
-# for a new user with no ssh or gpg keys, this is done logging in with `ssh -A` instead of `su`
-python3 -m poetry install
-cd
-# copy sample data
-cp -r /home/share/t15 .
-example_file="$HOME/t15/GMR_SS02113@UAS_Chrimson_Venus_X_0070/r_LED100_30s2x15s30s#n#n#n@100/20140918_170215/20140918_170215@GMR_SS02113@UAS_Chrimson_Venus_X_0070@t15@r_LED100_30s2x15s30s#n#n#n@100.spine"
-# make a `larvatagger` command
-if [ $USER = anzhou ]; then
-# for user 1
-port=9285
-else
-# for user 2
-port=9286
-fi
-if ! [ -f ~/.bash_aliases ] || [ -z "$(grep 'alias larvatagger=' ~/.bash_aliases)" ]; then
-echo "alias larvatagger='$HOME/LarvaTagger/scripts/larvatagger.jl open \"${example_file}\" --port=${port} --backends=\"$HOME/LarvaTagger\"'" >> ~/.bash_aliases
-fi
-# let the user know about the latter command on every login
-if [ -z "$(grep 'echo start the Nyx' ~/.bashrc)" ]; then
-cat <<EOT >> ~/.bashrc
-echo start the Nyx tagging UI with command: larvatagger
-echo or, for a richer interface, type: larvatagger.jl
-EOT
-fi