Add TLDR module
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Here is quick guide to add your script into TLDR interface
Scripts
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