Customizations for our GenoLogics BaseSpace Clarity LIMS
These are located on the server in the directory /opt/gls/clarity/customextensions
The owner of this directory is user glsjboss and the group claritylims.
All files and directories in this directory should be created and modified as the glsjboss user.
All git commands (commits, push, pull) should be done as your own user (that is, su user.name or log in as your own user and then run the relevant git commands.
To be able to do this, your user should be added to the claritylims group:
usermod -a -G claritylims user.name
You will need to log in and out to apply this change.
You may also need to adjust the write permissions on the .git directory to allow the group to write to it:
sudo chmod -R 775 .git
In the case that you want to commit as your own user from the glsjboss user, there is this command:
GIT_COMMITTER_NAME="New Name" GIT_COMMITTER_EMAIL="[email protected]" git commit --author="New Name <[email protected]>"
The automations here are input into the LIMS through the web interface.
They should first be modified through the files in this directory, and then copy-pasted into the web interface. This of course isn't always going to be the most practical workflow when playing around with automations, but it is recommended in order to keep the automations up to date in the git repository. Alternatively, one could copy paste from the web interface into the repository once sure the automation is sound, and then commit the changes.
The basic layout of an automation file should look like this:
# Clarity LIMS 5.0 Automation
## Modify the command in here first, and then copy-paste to the web interface.
## This will help keep the git repository up to date.
### Automation Name:
Assign QC Flags
### Creation date:
2018-03-09
### Author:
Kim Wong
### Enabled on master steps:
PicoGreen QC (DNA) 5.0
QuantIt BroadRange
QuantIt HighSensitivity
### Command:
bash -c "python /opt/gls/clarity/customextensions/assignqcflags.py -u {username} -p {password} -o '{udf:Criteria 1 - Operator}' -t '{udf:Criteria 1 - Threshold Value}' -a '{artifactsURI:v2}' -x '{outputFileLuids}'"
Make sure this file is updated to reflect changes in the web interface!
Scripts in Python are much easier to write with the SciLifeLab Genologics package. This was installed through ./pip install genologics (not ./conda install genologics as it doesn't exist in the conda repos) in the Miniconda environment /opt/gls/clarity/miniconda3/bin.
The config file for this package is found at /etc/genologics.conf, owned by root but readable for other users.
The clarity-ext package is designed to make writing extensions that are easier to read an simple to write. They have a higher level of abstraction than the genologics package, which has a 1-1 mapping to the REST API. Some of the scripts (all related to Covid19) are written using that framework.
Extensions that use this framework are all in ./clarity-ext-scripts. Refer to the README for more information on this package.
There is a client for SmiNet integration in ./sminet_client/. Refer to the README for more information on the package.
More information about the LIMS system including details on the Miniconda installation and starting the server may be found here.