AWS:Submit docking job - Revision history

Btingle: /* auto aws configure */

2022-10-11T22:11:08Z

auto aws configure

← Older revision		Revision as of 22:11, 11 October 2022
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	<nowiki>		<nowiki>
	docker run --rm -it -v /var/run/docker.sock:/var/run/docker.sock --env-file aws_config.txt ~~btingle~~/aws-setup</nowiki>		docker run --rm -it -v /var/run/docker.sock:/var/run/docker.sock --env-file aws_config.txt dockingorg/aws-setup</nowiki>

	== Monitoring Jobs ==		== Monitoring Jobs ==

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2022-09-14T21:22:46Z

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← Older revision		Revision as of 21:22, 14 September 2022
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			* Tutorial 1: [[AWS:Set up account]]
	~~Part~~ 2 ~~of 3 of the AWS docking tutorial~~		* Tutorial 2: [[AWS:Upload files for docking]]
			* Tutorial 3: AWS:Submit docking job THIS TUTORIAL
	~~Previous tutorial~~: [[AWS ~~DOCK Environment Setup~~]]		* Tutorial 4: [[AWS:Merge and download results]]
			* Tutorial 5: [[AWS:Cleanup]]
	~~Next~~ Tutorial: [[~~Docking Analysis On~~ AWS]]

	[[AWS:~~Upload files for docking~~]]

	= Quickstart- Submitting docking jobs through AWS =		= Quickstart- Submitting docking jobs through AWS =

Frodo: Frodo moved page Docking Submission On AWS to AWS:Submit docking job: clarity

2022-09-14T20:39:00Z

Frodo moved page Docking Submission On AWS to AWS:Submit docking job: clarity

← Older revision

Revision as of 20:39, 14 September 2022

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2022-09-14T20:35:29Z

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 Next Tutorial: [[Docking Analysis On AWS]]
-= Prerequisites =
+[[AWS:Upload files for docking]]
 = Quickstart- Submitting docking jobs through AWS =

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2022-09-14T17:01:39Z

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← Older revision		Revision as of 17:01, 14 September 2022
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	~~[[Category:AWS DOCK]]~~

	Part 2 of 3 of the AWS docking tutorial		Part 2 of 3 of the AWS docking tutorial
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	Every billing cycle you can request AWS to increase your spot instance limit some more. This may take some time, but just make sure to explain your use case in the form and they will be more than happy to oblige.		Every billing cycle you can request AWS to increase your spot instance limit some more. This may take some time, but just make sure to explain your use case in the form and they will be more than happy to oblige.

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

Btingle: /* Alternative DOCK Executable */

2022-08-02T21:07:31Z

Alternative DOCK Executable

← Older revision		Revision as of 21:07, 2 August 2022
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	<nowiki>		<nowiki>
			# replace path here with the URI to your special executable
	$ export S3_DOCKEXEC_LOCATION=s3://mybucket/dock_alternatives/special1/dock64		$ export S3_DOCKEXEC_LOCATION=s3://mybucket/dock_alternatives/special1/dock64
	$ bash supersub.bash </nowiki>		$ bash supersub.bash </nowiki>

Btingle at 19:32, 28 July 2022

2022-07-28T19:32:43Z

← Older revision		Revision as of 19:32, 28 July 2022
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	= Quickstart- Submitting docking jobs through AWS =		= Quickstart- Submitting docking jobs through AWS =

	== ~~Prerequisites~~ ==		== Setup ==

	=== Upload Dockfiles ===		=== Upload Dockfiles ===
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	Once your input list has been prepared, upload it to S3 using your preferred method. Make sure to copy the S3 URI for your input list file, it will be used during submission.		Once your input list has been prepared, upload it to S3 using your preferred method. Make sure to copy the S3 URI for your input list file, it will be used during submission.

	== Note for first-time runs ==		=== Note for first-time runs ===

	Prior to submitting a large docking campaign, it is wise to prepare a smaller run first, to check that the configuration etc. are working properly. You don't want to spend oodles of money on a docking campaign that didn't produce anything due to a broken configuration.		Prior to submitting a large docking campaign, it is wise to prepare a smaller run first, to check that the configuration etc. are working properly. You don't want to spend oodles of money on a docking campaign that didn't produce anything due to a broken configuration.

	== ~~Quick Start~~ ==		== Job Submission ==

	This step takes place in the aws-setup container. Run aws configure on startup as per usual. If you'd like to avoid running configure on start-up every time, see the "auto aws configure" subsection at the bottom.		This step takes place in the aws-setup container. Run aws configure on startup as per usual. If you'd like to avoid running configure on start-up every time, see the "auto aws configure" subsection at the bottom.

Btingle: /* Quickstart- Submitting docking jobs through AWS */

2022-07-28T19:28:31Z

Quickstart- Submitting docking jobs through AWS

← Older revision		Revision as of 19:28, 28 July 2022
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	= Quickstart- Submitting docking jobs through AWS =		= Quickstart- Submitting docking jobs through AWS =

	This step takes place in the aws-setup container. Run aws configure on startup as per usual. If you'd like to avoid running configure on start-up every time, see the "auto aws configure" subsection at the bottom.

	== Prerequisites ==		== Prerequisites ==
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	== Quick Start ==		== Quick Start ==

			This step takes place in the aws-setup container. Run aws configure on startup as per usual. If you'd like to avoid running configure on start-up every time, see the "auto aws configure" subsection at the bottom.

	Run supersub.bash without any arguments		Run supersub.bash without any arguments

Btingle at 19:28, 28 July 2022

2022-07-28T19:28:10Z

← Older revision		Revision as of 19:28, 28 July 2022
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	* Likewise, you will need to know your AWS access key, secret key, etc.		* Likewise, you will need to know your AWS access key, secret key, etc.

	== ~~Copying~~ data to Amazon S3 ==		== How to copy data to Amazon S3 ==

	In the previous tutorial, you created an S3 bucket to set up your environment. S3 buckets act like virtual hard drives, with familiar operations like cp, ls, rm, and mv for storing & manipulating data.		In the previous tutorial, you created an S3 bucket to set up your environment. S3 buckets act like virtual hard drives, with familiar operations like cp, ls, rm, and mv for storing & manipulating data.
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	You can take one of two approaches to get your data into an S3 bucket; the first is less complicated and more intuitive, the second is more complicated but opens more avenues for automation.		You can take one of two approaches to get your data into an S3 bucket; the first is less complicated and more intuitive, the second is more complicated but opens more avenues for automation.

	==== Approach 1: Use the browser console ====		=== Approach 1: Use the browser console ===

	AWS allows uploading files to S3 directly from the browser. Navigate to the S3 console (https://s3.console.aws.amazon.com/s3), where there should be a list of all buckets that your account owns.		AWS allows uploading files to S3 directly from the browser. Navigate to the S3 console (https://s3.console.aws.amazon.com/s3), where there should be a list of all buckets that your account owns.
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	You can click "Copy S3 Uri" in the top right of the interface to copy the full path of the directory or file you are viewing.		You can click "Copy S3 Uri" in the top right of the interface to copy the full path of the directory or file you are viewing.

	==== Approach 2: AWS CLI ====		=== Approach 2: AWS CLI ===

	The AWS CLI provides an interface to perform any conceivable operation on AWS resources, including S3 buckets.		The AWS CLI provides an interface to perform any conceivable operation on AWS resources, including S3 buckets.
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	This step takes place in the aws-setup container. Run aws configure on startup as per usual. If you'd like to avoid running configure on start-up every time, see the "auto aws configure" subsection at the bottom.		This step takes place in the aws-setup container. Run aws configure on startup as per usual. If you'd like to avoid running configure on start-up every time, see the "auto aws configure" subsection at the bottom.

	==~~== Note for first-time runs ==~~==		== Prerequisites ==

	Prior to submitting a large docking campaign, it is wise to prepare a smaller run first, to check that the configuration etc. are working properly. You don't want to spend oodles of money on a docking campaign that didn't produce anything due to a broken configuration.		=== Upload Dockfiles ===

	~~==== Requirements ====~~		Using your preferred method, upload your dockfiles to S3. Make sure to copy the S3 URI for your dockfiles folder, it will be used during submission. INDOCK configuration is expected to be located within the dockfiles folder.

	* Have dockfiles uploaded to S3, as well as the S3 object URL for the folder.		=== Upload Input List ===
	* Have an input list uploaded to S3, and have the S3 object URL for that list.

	The input list may need some explanation. This input list is expected to be a text file containing a list of S3 paths to dockable db2.tgz files accessible by the environment you are submitting to. For example, here is a short but valid input list:		The input list may need some explanation. This input list is expected to be a text file containing a list of S3 paths to dockable db2.tgz files accessible by the environment you are submitting to. For example, here is a short but valid input list:
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	If you would like to create your own list, it is possible to select molecules to DOCK through our tranches viewer, available on cartblanche: https://cartblanche22.docking.org/tranches/3d. Use the interface to select molecules based on heavy atoms, charge, and logP. Once your selection is ready, click the download button in the top right to open the download menu. Under "method", select "DOCK37 (*.db2.tgz)" and "AWS S3" then confirm the download. This file can be used as an input list.		If you would like to create your own list, it is possible to select molecules to DOCK through our tranches viewer, available on cartblanche: https://cartblanche22.docking.org/tranches/3d. Use the interface to select molecules based on heavy atoms, charge, and logP. Once your selection is ready, click the download button in the top right to open the download menu. Under "method", select "DOCK37 (*.db2.tgz)" and "AWS S3" then confirm the download. This file can be used as an input list.

	==== Quick Start ====		Once your input list has been prepared, upload it to S3 using your preferred method. Make sure to copy the S3 URI for your input list file, it will be used during submission.

			== Note for first-time runs ==

			Prior to submitting a large docking campaign, it is wise to prepare a smaller run first, to check that the configuration etc. are working properly. You don't want to spend oodles of money on a docking campaign that didn't produce anything due to a broken configuration.

			== Quick Start ==

	Run supersub.bash without any arguments		Run supersub.bash without any arguments

Btingle at 19:22, 28 July 2022

2022-07-28T19:22:05Z

← Older revision		Revision as of 19:22, 28 July 2022
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	Next Tutorial: [[Docking Analysis On AWS]]		Next Tutorial: [[Docking Analysis On AWS]]

	== Prerequisites ==		= Prerequisites =

	* You've followed the tutorial for setting up the environment: [[AWS DOCK Environment Setup]]		* You've followed the tutorial for setting up the environment: [[AWS DOCK Environment Setup]]
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	Note- if you're a Mac user, there may be some pain with permissions during this step. Your Mac will want you to provide explicit permissions for docker to access the linked directory, here's the docker tutorial on how to fix this: https://docs.docker.com/desktop/mac/#file-sharing.		Note- if you're a Mac user, there may be some pain with permissions during this step. Your Mac will want you to provide explicit permissions for docker to access the linked directory, here's the docker tutorial on how to fix this: https://docs.docker.com/desktop/mac/#file-sharing.

	=~~= Running supersub.bash =~~=		= Quickstart- Submitting docking jobs through AWS =

	This step takes place in the aws-setup container. Run aws configure on startup as per usual. If you'd like to avoid running configure on start-up every time, see the "auto aws configure" subsection at the bottom.		This step takes place in the aws-setup container. Run aws configure on startup as per usual. If you'd like to avoid running configure on start-up every time, see the "auto aws configure" subsection at the bottom.