AWS:Merge and download results - Revision history

Frodo: asdf

2022-09-14T21:30:00Z

asdf

← Older revision		Revision as of 21:30, 14 September 2022
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	* Tutorial 1: [[AWS:Set up account]]		* Tutorial 1: [[AWS:Set up account]]
	* Tutorial 2: [[AWS:Upload files for docking]]		* Tutorial 2: [[AWS:Upload files for docking]]
	* Tutorial 3: AWS:Submit docking job ~~THIS TUTORIAL~~		* Tutorial 3: [[AWS:Submit docking job]]
	* Tutorial 4: [[AWS:Merge and download results]]		* Tutorial 4: AWS:Merge and download results THIS TUTORIAL
	* Tutorial 5: [[AWS:Cleanup]]		* Tutorial 5: [[AWS:Cleanup]]

2022-09-14T21:23:19Z

asdf

← Older revision		Revision as of 21:23, 14 September 2022
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			* Tutorial 1: [[AWS:Set up account]]
			* Tutorial 2: [[AWS:Upload files for docking]]
			* Tutorial 3: AWS:Submit docking job THIS TUTORIAL
			* Tutorial 4: [[AWS:Merge and download results]]
			* Tutorial 5: [[AWS:Cleanup]]

	~~Part 3 of 3 of the AWS docking tutorial~~

	~~Previous Tutorial: [[Docking Submission On AWS]]~~

	=== Prerequisites ===		=== Prerequisites ===

2022-09-14T20:41:20Z

← Older revision

Revision as of 20:41, 14 September 2022

2022-09-14T17:02:07Z

asdf

← Older revision		Revision as of 17:02, 14 September 2022
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	~~[[Category:AWS DOCK]]~~

	Part 3 of 3 of the AWS docking tutorial		Part 3 of 3 of the AWS docking tutorial
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	[[File:Terminateinstance.png\|frameless]]		[[File:Terminateinstance.png\|frameless]]

			[[Category:AWS]]
			[[Category:DOCK 3.8]]
			[[Category:Tutorial]]

2022-08-03T22:43:52Z

Step 4: Run Analysis and save results

← Older revision		Revision as of 22:43, 3 August 2022
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	python3.8 ~/DOCK/ucsfdock/analysis/top_poses/top_poses.py ~/data/5HT2A/H17 -n 10000 -o ~/data/5HT2A/poses_H17 -j 1</nowiki>		python3.8 ~/DOCK/ucsfdock/analysis/top_poses/top_poses.py ~/data/5HT2A/H17 -n 10000 -o ~/data/5HT2A/poses_H17 -j 1</nowiki>

	There is no need to provide a dirlist, top_poses.py will find all test.mol2* files beneath the directory you specify. Alternatively you can provide a text file containing a list of test.mol2* files to analyze.		This command, for example fetches the top 10,000 scoring molecules found in test.mol2.gz* files underneath the ~/data/5HT2A/poses_H17 directory on one core. See the linked wiki page for more details.

			There is no need to provide a dirlist, top_poses.py will find all test.mol2* files beneath the directory you specify. Alternatively you can provide a text file containing a list of test.mol2.gz* files to analyze.

	Two files will be created, a .mol2.gz file and a .scores file. The .mol2.gz file will contain the mol2 data for all top poses, and .scores will contain a text line for each top pose describing energy etc parameters.		Two files will be created, a .mol2.gz file and a .scores file. The .mol2.gz file will contain the mol2 data for all top poses, and .scores will contain a text line for each top pose describing energy etc parameters.

2022-07-29T20:24:40Z

← Older revision		Revision as of 20:24, 29 July 2022
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	DOCK:		DOCK:
	<nowiki>		<nowiki>
	git clone https://github.com/docking-org/DOCK.git</nowiki>		$ git clone https://github.com/docking-org/DOCK.git
			Cloning into 'DOCK'...
			Username for 'https://github.com': myuser
			Password for 'https://myuser@github.com': <paste your github access token here></nowiki>

	python3.8:		python3.8:

2022-07-28T19:37:54Z

Prerequisites

← Older revision		Revision as of 19:37, 28 July 2022
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	=== Prerequisites ===		=== Prerequisites ===

	github personal access token & DOCK repository access rights (https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token)		github personal access token & DOCK github repository access rights (https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token)

			You will need to provide this access token as a password when pulling the DOCK repository. You can email us at bkslab for access to the DOCK repository.

	aws account & credentials (https://docs.aws.amazon.com/general/latest/gr/aws-sec-cred-types.html#access-keys-and-secret-access-keys)		aws account & credentials (https://docs.aws.amazon.com/general/latest/gr/aws-sec-cred-types.html#access-keys-and-secret-access-keys)

2022-07-27T05:38:48Z

← Older revision		Revision as of 05:38, 27 July 2022
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	Part 3 of 3 of the AWS docking tutorial		Part 3 of 3 of the AWS docking tutorial

	Previous Tutorial: [[Docking ~~Analysis~~ On AWS]]		Previous Tutorial: [[Docking Submission On AWS]]

	=== Prerequisites ===		=== Prerequisites ===

2022-07-27T05:38:28Z

2022-07-27T05:38:12Z

← Older revision		Revision as of 05:38, 27 July 2022
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	[[Category:AWS DOCK]]		[[Category:AWS DOCK]]

			[[Category:AWS DOCK]]

			Part 3 of 3 of the AWS docking tutorial

			Previous Tutorial: [[Docking Analysis On AWS]]

	=== Prerequisites ===		=== Prerequisites ===