Add TLDR module

Here is quick guide to add your script into TLDR interface

Add job type into psql table

• Access the database

$ psql -h mem2 -d blaster -U blasteruser

• Look for the next available index on job_types table

blaster=> select * from job_types order by job_type_id;
You will see table like this
job_type_id |        last_updated        |      short_name      | hidden | approval_required | job_type_status_fk | description
------------+----------------------------+----------------------+--------+-------------------+--------------------+------------------------------------------------------------------------------------------------
         34 | 2024-03-07 09:48:22.442957 | build3d_covalent     | f      | f                 |                  2 | Build db2 for covalent library using DOCK3.7 pipeline.
         33 | 2023-02-08 10:17:11.904655 | dockopt2             | t      | f                 |                  3 | Prepare receptor for docking and perform basic controls from SMILES inputs. This is retrodocking without optimization. Results can be used for Large Scale Docking.

• Insert new job type (Please be extra careful when doing this step)

This is important to start command with 'begin;' so that if any syntax mistakes could be undo.
blaster=> begin; insert into job_types values(<next_available_id>, now(), '<job_shortname>', true, false, 1, <description>);
Example: 
blaster=> begin; insert into job_types values(16, now(), 'shape', true, false, 1, 'look up molecule based on molecular shape using FastROCS');
//To save data
blaster=> commit;
//Or if made mistake, to reverse cmd
blaster=> rollback;

Setting up templates

• Create template directory

sudo -i
su - www 
cd /nfs/ex7/blaster/templates/
mkdir <job_name> # job_name must match the shortname in job_types table
chmod 777 job_name #for now... 

• Get parameters.json

This is recommend that you go though all the currently existing modules on TLDR and reuse instead of starting one from scratch.

cd job_name
cp <whatever parameters.json you pick>
vim parameters.json
Change the variables. Check on the website if the module shows up.

• Move your shell scripts in directory