Add TLDR module: Difference between revisions
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Here is quick guide to add your script into [[ | Here is quick guide to add your script into [[TLDR]] interface | ||
=== Scripts === | === Scripts === | ||
=== Add job type into psql table === | === Add job type into psql table === | ||
*Access the database | *Access the database | ||
$ psql -h | $ psql -h mem2 -d blaster -U blasteruser | ||
*Look for the next available index on job_types table | *Look for the next available index on job_types table | ||
blaster=> select * from job_types order by job_type_id; | blaster=> select * from job_types order by job_type_id; | ||
You will see table like this | 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) | * 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.''' | '''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(), '< | blaster=> begin; insert into job_types values(<next_available_id>, now(), '<job_shortname>', true, false, 1, <description>); | ||
Example: | Example: | ||
blaster=> begin; insert into job_types values(16, now(), 'shape'); | 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 === | ||
This is recommend that you go though all the currently existing modules on [ | * 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 [https://tldr.docking.org 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 | |||
=== Test run! === | |||
[[Category: Developer]] | |||
[[Category: TLDR]] | |||
Latest revision as of 18:12, 14 January 2025
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