Add Tools18 module: Difference between revisions
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=== 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 | ||
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Example: | Example: | ||
blaster=> begin; insert into job_types values(16, now(), 'shape'); | blaster=> begin; insert into job_types values(16, now(), 'shape'); | ||
//To save data | |||
blaster=> commit; | |||
//Or if made mistake, to reserve cmd | |||
blaster=> rollback; | |||
=== Setting up templates === | === Setting up templates === | ||
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$ chmod 777 job_name //for now... | $ chmod 777 job_name //for now... | ||
* Get parameters.json | * Get parameters.json | ||
This is recommend that you go though all the currently existing modules on [ | 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 | $ cd job_name | ||
$ cp <whatever parameters.json you pick> | $ cp <whatever parameters.json you pick> | ||
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=== Test run! === | === Test run! === | ||
[[Category: Developer]] | |||
[[Category: TLDR]] |
Latest revision as of 19:30, 18 October 2022
Here is quick guide to add your script into Tools18 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 -------------+----------------------------+------------------- 1 | 2018-10-05 00:00:00 | analog 2 | 2018-10-05 00:00:00 | blaster 3 | 2018-10-05 00:00:00 | blasterpdb 4 | 2018-10-05 00:00:00 | build2d 5 | 2018-10-05 00:00:00 | build3d 6 | 2018-10-05 00:00:00 | cluster 7 | 2018-10-05 00:00:00 | covalent 8 | 2018-10-05 00:00:00 | dude 9 | 2018-10-05 00:00:00 | libanalysis 10 | 2018-10-05 00:00:00 | reaction 11 | 2018-10-05 00:00:00 | sea 12 | 2018-10-05 00:00:00 | threec 13 | 2018-10-05 00:00:00 | transform 14 | 2018-10-05 00:00:00 | zincbatch 15 | 2018-12-01 18:47:34 | cluster_molecules
- 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(), '<your_job_name>'); Example: blaster=> begin; insert into job_types values(16, now(), 'shape'); //To save data blaster=> commit; //Or if made mistake, to reserve cmd blaster=> rollback;
Setting up templates
- Create directory
$ 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