Add Tools18 module

Here is quick guide to add your script into Tools18 interface

Add job type into psql table

• Access the database

$ psql -h mem blaster 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 Tools18 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: Tools18]]