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(Created page with "Here is quick guide to add your script into Tools18 interface === Scripts === === Creating Template === === Add job type into psql table === === Test run! ===")
 
(Test run!)
 
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Here is quick guide to add your script into [[Tools18]] interface
 
Here is quick guide to add your script into [[Tools18]] interface
 
=== Scripts ===
 
=== Scripts ===
=== Creating Template ===
+
 
 
=== Add job type into psql table ===
 
=== 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 [http://tools18.docking.org/start 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! ===
 
=== Test run! ===
 +
 +
[[Category: Tools18]]
 +
[[Category: TLDR]]

Latest revision as of 10:13, 27 May 2020

Here is quick guide to add your script into Tools18 interface

Scripts

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!