TLDR - Revision history

Khtang: /* Supported field types */

2025-02-13T20:15:27Z

Supported field types

← Older revision		Revision as of 20:15, 13 February 2025
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	[[Category: TLDR]]		[[Category: TLDR]]
	[[Category: ~~Tools18~~]]		[[Category: Khanh]]

Khtang at 23:31, 6 January 2025

2025-01-06T23:31:00Z

← Older revision		Revision as of 23:31, 6 January 2025
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	TLDR (TLDR is a Ligand Discovery Resource, tldr.docking.org) is a web-based interface to molecular docking, cheminformatics and related tools. The system currently consists of a dozen or so apps. We plan to support dozens, perhaps a hundred.		TLDR (TLDR is a Ligand Discovery Resource, tldr.docking.org) is a web-based interface to molecular docking, cheminformatics and related tools. The system currently consists of a dozen or so apps. We plan to support dozens, perhaps a hundred.

			{{TOCright}}

	== Advantages ==		== Advantages ==
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	This is also called "Add TLDR Module"		This is also called "Add TLDR Module"

	~~{{TOCright}}~~

	== Current available modules ==		== Current available modules ==

Khtang: /* Current available modules */

2024-11-12T06:21:45Z

Current available modules

← Older revision		Revision as of 06:21, 12 November 2024
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	* [[TLDR:bootstrap1\|Bootstrap1]]		* [[TLDR:bootstrap1\|Bootstrap1]]
	* [[TLDR:bootstrap2\|Bootstrap2]]		* [[TLDR:bootstrap2\|Bootstrap2]]
	* [[TLDR:~~dude-z~~\|DUDE-Z]]		* [[TLDR:dudez\|DUDE-Z]]
	* [[TLDR:extrema\|Extrema]]		* [[TLDR:extrema\|Extrema]]
	* [[TLDR:~~newbuild3d~~\|~~Newbuild3d~~]]		* [[TLDR:build3d38\|Build3d38]]
	* [[TLDR:strain\|Strain]]		* [[TLDR:strain\|Strain]]
	* [[TLDR:swbatch\|Swbatch]]		* [[TLDR:swbatch\|Swbatch]]

Frodo: asdf

2024-05-24T01:36:02Z

asdf

← Older revision		Revision as of 01:36, 24 May 2024
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	TLDR (tldr.docking.org) is a web-based interface to molecular docking and related tools.		TLDR (TLDR is a Ligand Discovery Resource, tldr.docking.org) is a web-based interface to molecular docking, cheminformatics and related tools. The system currently consists of a dozen or so apps. We plan to support dozens, perhaps a hundred.
	The system currently consists of a dozen apps. We plan to support dozens, perhaps a hundred ~~all told~~.
			== Advantages ==
			* you don't need to install

			== Disadvantages ==
			* limited control
			* limited by access to our servers
			* competition with other users

	Here we list the apps you can currently use, with usage notes.		Here we list the apps you can currently use, with usage notes.

Frodo: /* Current available modules */ asdf

2024-04-29T20:27:13Z

Current available modules: asdf

← Older revision		Revision as of 20:27, 29 April 2024
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	== Current available modules ==		== Current available modules ==
	~~===~~ [[TLDR:arthorbatch\|Arthorbatch]] ~~===~~		* [[TLDR:arthorbatch\|Arthorbatch]]
			* [[TLDR:bioisostere\|Bioisostere]]
	~~===~~ [[TLDR:bioisostere\|Bioisostere]] ~~===~~		* [[TLDR:bootstrap1\|Bootstrap1]]
			* [[TLDR:bootstrap2\|Bootstrap2]]
	~~===~~ [[TLDR:bootstrap1\|Bootstrap1]] ~~===~~		* [[TLDR:dude-z\|DUDE-Z]]
			* [[TLDR:extrema\|Extrema]]
	~~===~~ [[TLDR:bootstrap2\|Bootstrap2]] ~~===~~		* [[TLDR:newbuild3d\|Newbuild3d]]
			* [[TLDR:strain\|Strain]]
	~~===~~ [[TLDR:dude-z\|DUDE-Z]] ~~===~~		* [[TLDR:swbatch\|Swbatch]]

	~~===~~ [[TLDR:extrema\|Extrema]] ~~===~~

	~~===~~ [[TLDR:newbuild3d\|Newbuild3d]] ~~===~~

	~~===~~ [[TLDR:strain\|Strain]] ~~===~~

	~~===~~ [[TLDR:swbatch\|Swbatch]] ~~===~~

	== In Development ==		== In Development ==

Btingle: /* Making changes to modules & scripts */

2023-05-18T18:57:10Z

Making changes to modules & scripts

← Older revision		Revision as of 18:57, 18 May 2023
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	modules are located @ /nfs/ex7/tldr-modules		modules are located @ /nfs/ex7/tldr-modules

			input files & parameters are defined by parameters.json within the module directory

	modules are fairly straightforward bash scripts that operate in a designated working directory created by tldr when a job is submitted		modules are fairly straightforward bash scripts that operate in a designated working directory created by tldr when a job is submitted

Btingle: /* Making changes to modules & scripts */

2023-05-18T18:56:46Z

Making changes to modules & scripts

← Older revision		Revision as of 18:56, 18 May 2023
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	the specific 0-9 directory the job directory is located in is based on the last digit of the tldr-provided job_id- these directories are striped across multiple disks		the specific 0-9 directory the job directory is located in is based on the last digit of the tldr-provided job_id- these directories are striped across multiple disks

			within the job's working directory "results" is a special directory that will be shown to the user containing results

	=== TLDR database ===		=== TLDR database ===

Btingle: /* How to open source code & make a change */

2023-05-18T18:55:45Z

How to open source code & make a change

← Older revision		Revision as of 18:55, 18 May 2023
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	1. unpack most recent distribution in dist folder to your preferred directory		1. unpack most recent distribution in dist folder to your preferred directory

	2. make changes to source code. this is left as an exercise for the reader		2. make changes to source code. this is left as an exercise for the reader

	3. once done, re-pack source code into tarball. if you want to change the version name, change the name of the source code's root directory & dist package- for organizational purposes		3. once done, re-pack source code into tarball. if you want to change the version name, change the name of the source code's root directory & dist package- for organizational purposes

	4. copy the package back to the tldr dist directory- not strictly necessary, but again, for organizational purposes		4. copy the package back to the tldr dist directory- not strictly necessary, but again, for organizational purposes

	5. with the tldr python environment, pip install the package you just created		5. with the tldr python environment, pip install the package you just created

	* /nfs/soft/www/home/apps/tools18/envs/tldr-prod/bin/python3.9 -m pip install /nfs/soft/www/home/apps/tools18/dist/$YOUR_PACKAGE		* /nfs/soft/www/home/apps/tools18/envs/tldr-prod/bin/python3.9 -m pip install /nfs/soft/www/home/apps/tools18/dist/$YOUR_PACKAGE

	* this will uninstall the previous version- I haven't tried doing this while the server is live, but it should probably(?) be fine		* this will uninstall the previous version- I haven't tried doing this while the server is live, but it should probably(?) be fine

	6. restart the tldr webserver on gimel2		6. restart the tldr webserver on gimel2

	* supervisorctl restart tldr		* supervisorctl restart tldr

Btingle: /* Technical info */

2023-05-18T18:55:20Z

Technical info

← Older revision		Revision as of 18:55, 18 May 2023
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	= Technical info =		= Technical info =

	Ben's info section ~~on how to make changes:~~		== Ben's info section ==

	python environment is @ /nfs/soft/www/home/apps/tools18/envs/tldr-prod/bin/python3.9		python environment is @ /nfs/soft/www/home/apps/tools18/envs/tldr-prod/bin/python3.9
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	tldr distribution packages are @ /nfs/soft/www/home/apps/tools18/dist		tldr distribution packages are @ /nfs/soft/www/home/apps/tools18/dist

	== How to open source code & make a change ==		=== How to open source code & make a change ===

	1. unpack most recent distribution in dist folder to your preferred directory		1. unpack most recent distribution in dist folder to your preferred directory
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	* supervisorctl restart tldr		* supervisorctl restart tldr

	== Making changes to modules & scripts ==		=== Making changes to modules & scripts ===

	modules are located @ /nfs/ex7/tldr-modules		modules are located @ /nfs/ex7/tldr-modules
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	the specific 0-9 directory the job directory is located in is based on the last digit of the tldr-provided job_id- these directories are striped across multiple disks		the specific 0-9 directory the job directory is located in is based on the last digit of the tldr-provided job_id- these directories are striped across multiple disks

	== TLDR database ==		=== TLDR database ===

	psql -h mem2 -p 5432 -d blaster -U blasteruser		psql -h mem2 -p 5432 -d blaster -U blasteruser

Btingle at 18:54, 18 May 2023

2023-05-18T18:54:44Z

← Older revision		Revision as of 18:54, 18 May 2023
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	= Technical info =		= Technical info =

			Ben's info section on how to make changes:

			python environment is @ /nfs/soft/www/home/apps/tools18/envs/tldr-prod/bin/python3.9

			tldr distribution packages are @ /nfs/soft/www/home/apps/tools18/dist

			== How to open source code & make a change ==

			1. unpack most recent distribution in dist folder to your preferred directory
			2. make changes to source code. this is left as an exercise for the reader
			3. once done, re-pack source code into tarball. if you want to change the version name, change the name of the source code's root directory & dist package- for organizational purposes
			4. copy the package back to the tldr dist directory- not strictly necessary, but again, for organizational purposes
			5. with the tldr python environment, pip install the package you just created
			* /nfs/soft/www/home/apps/tools18/envs/tldr-prod/bin/python3.9 -m pip install /nfs/soft/www/home/apps/tools18/dist/$YOUR_PACKAGE
			* this will uninstall the previous version- I haven't tried doing this while the server is live, but it should probably(?) be fine
			6. restart the tldr webserver on gimel2
			* supervisorctl restart tldr

			== Making changes to modules & scripts ==

			modules are located @ /nfs/ex7/tldr-modules

			modules are fairly straightforward bash scripts that operate in a designated working directory created by tldr when a job is submitted

			job files are stored in /nfs/ex7/blaster/jobs/[0-9]

			the specific 0-9 directory the job directory is located in is based on the last digit of the tldr-provided job_id- these directories are striped across multiple disks

			== TLDR database ==

			psql -h mem2 -p 5432 -d blaster -U blasteruser

			can add new modules by adding to the job_types table
			set module private/public by modifying job_type_status_fk in this table

	== starting the server in single-threaded mode ==		== starting the server in single-threaded mode ==

← Older revision		Revision as of 06:21, 12 November 2024
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	* [[TLDR:bootstrap1\|Bootstrap1]]		* [[TLDR:bootstrap1\|Bootstrap1]]
	* [[TLDR:bootstrap2\|Bootstrap2]]		* [[TLDR:bootstrap2\|Bootstrap2]]
	* [[TLDR:~~dude-z~~\|DUDE-Z]]		* [[TLDR:dudez\|DUDE-Z]]
	* [[TLDR:extrema\|Extrema]]		* [[TLDR:extrema\|Extrema]]
	* [[TLDR:~~newbuild3d~~\|~~Newbuild3d~~]]		* [[TLDR:build3d38\|Build3d38]]
	* [[TLDR:strain\|Strain]]		* [[TLDR:strain\|Strain]]
	* [[TLDR:swbatch\|Swbatch]]		* [[TLDR:swbatch\|Swbatch]]

← Older revision		Revision as of 20:27, 29 April 2024
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	== Current available modules ==		== Current available modules ==
	~~===~~ [[TLDR:arthorbatch\|Arthorbatch]] ~~===~~		* [[TLDR:arthorbatch\|Arthorbatch]]
			* [[TLDR:bioisostere\|Bioisostere]]
	~~===~~ [[TLDR:bioisostere\|Bioisostere]] ~~===~~		* [[TLDR:bootstrap1\|Bootstrap1]]
			* [[TLDR:bootstrap2\|Bootstrap2]]
	~~===~~ [[TLDR:bootstrap1\|Bootstrap1]] ~~===~~		* [[TLDR:dude-z\|DUDE-Z]]
			* [[TLDR:extrema\|Extrema]]
	~~===~~ [[TLDR:bootstrap2\|Bootstrap2]] ~~===~~		* [[TLDR:newbuild3d\|Newbuild3d]]
			* [[TLDR:strain\|Strain]]
	~~===~~ [[TLDR:dude-z\|DUDE-Z]] ~~===~~		* [[TLDR:swbatch\|Swbatch]]

	~~===~~ [[TLDR:extrema\|Extrema]] ~~===~~

	~~===~~ [[TLDR:newbuild3d\|Newbuild3d]] ~~===~~

	~~===~~ [[TLDR:strain\|Strain]] ~~===~~

	~~===~~ [[TLDR:swbatch\|Swbatch]] ~~===~~

	== In Development ==		== In Development ==