A Guix pack installation is a simple installation suitable for users
not interested in the Guix package manager. The detailed instructions
below follow the same process automated by the install script found
on the evaluate page, but provides
additional diagnostic information.
The first step in the install script is setting up the database.
Manually install the database using instructions on the postgres page.
If you are using the install script and
it is not executable, change permissions:
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chmod 777 install-limsn-pack.sh
Download and unzip the
archive
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wget https://github.com/labsolns/labsolns/releases/download/v0.1.0p/limsn-0.1.0-pack.tar.gz tar xf ./limsn-0.1.0-pack.tar.gz
Note that in the above example I am using the admin account on AWS so
$HOME == /home/admin
Initialize LIMS*Nucleus
Initialize by executing ./bin/init-limsn-pack.sh. The function of the
various scripts is described on the scripts page. Check that the
$HOME/.config/limsn directory has been created and artanis.conf has been
copied into the directory:
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$ ls$HOME/.config/limsn artanis.conf
Check that $HOME/.bashrc has been modified to include exports for
LC_ALL, PATH, GUILE_LOAD_PATH, and GUILE_DBD_PATH.
$HOME/.bashrc
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... $cat$HOME/.bashrc /# 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 export LC_ALL="C" export PATH=/home/admin/bin:/gnu/store/2rl49lcanmqn26s660dd85lv7pfn0ykb-limsn-0.1.0/bin:/home/admin/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games export GUILE_LOAD_PATH=/home/admin/gnu/store/rj0pzbki1m5hpcshs614mhkrgs2b3i9d-artanis-0.5.2/share/guile/site/3.0:/home/admin/gnu/store/780bll8lp0xvj7rnazb2qdnrnb329lbw-guile-json-3.5.0/share/guile/site/3.0:/home/admin/gnu/store/jmn100gjcpqbfpxrhrna6gzab8hxkc86-guile-redis-2.1.1/share/guile/site/3.0:/home/admin/gnu/store/3f0lv3m4vlzqc86750025arbskfrq05p-guile-dbi-2.1.8/share/guile/site/2.2 export GUILE_DBD_PATH=/home/admin/gnu/store/z5kilafxayw2kdvn3anw1shkqij17dqb-guile-dbd-postgresql-2.1.8/lib
source .bashrc to make certain that all environment variables have
been properly set:
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$source$HOME/.bashrc
Modify the
artanis.conf configuration file
Critical parameters are described on the configuration page. You must have in
hand IP addresses for the database and client.
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sudo nano $HOME/.config/limsn/artanis.conf
Make sure the
database is available and loaded
The psql command below will work on a local database - modify
accordingly. You should find 10 preloaded projects. Projects 4-9 are
empty and can be used for experimentation:
id | project_sys_name | descr | project_name | sessions_id | updated ----+------------------+------------------------------------------+----------------------+-------------+------------------------------- 1 | PRJ-1 | 3 plate sets with 2 96 well plates each | With AR, HL | 9999999999 | 2022-04-06 11:07:05.854606+00 2 | PRJ-2 | 1 plate set with 2 384 well plates each | With AR | 9999999999 | 2022-04-06 11:07:06.825439+00 3 | PRJ-3 | 1 plate set with 1 1536 well plate | With AR | 9999999999 | 2022-04-06 11:07:08.32809+00 4 | PRJ-4 | description 4 | MyTestProj4 | 9999999999 | 2022-04-06 11:07:13.364018+00 5 | PRJ-5 | description 5 | MyTestProj5 | 9999999999 | 2022-04-06 11:07:13.365426+00 6 | PRJ-6 | description 6 | MyTestProj6 | 9999999999 | 2022-04-06 11:07:13.367082+00 7 | PRJ-7 | description 7 | MyTestProj7 | 9999999999 | 2022-04-06 11:07:13.368542+00 8 | PRJ-8 | description 8 | MyTestProj8 | 9999999999 | 2022-04-06 11:07:13.370008+00 9 | PRJ-9 | description 9 | MyTestProj9 | 9999999999 | 2022-04-06 11:07:13.371613+00 10 | PRJ-10 | 2 plate sets with 10 96 well plates each | Plates only, no data | 9999999999 | 2022-04-06 11:07:13.372956+00 (10 rows)
lndb=>
Start LIMS*Nucleus
Start in detached mode so you can close the terminal. To kill the
process you will need to look up the PID and kill. Start in regular mode
to monitor any error messages.
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$nohup start-limsn.sh &
to kill Ctrl-C in interactive mode or in detached mode: