DOCK 3.8:How to build a release - Revision history

Kyle: /* Distribution */

2025-07-15T20:06:20Z

Distribution

← Older revision		Revision as of 20:06, 15 July 2025
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	= Distribution =		= Distribution =
	* ~~put~~ on ~~DOCK license server~~		* [[Add_major_version#Adding_new_DOCK_Versions_to_licensing.docking.org\|Put on licensing.docking.org]]
	* copy dock3.8.x.tar.gz to dock server. test download and install		* copy dock3.8.x.tar.gz to dock server. test download and install
	* put on gimel		* put on gimel

Frodo: /* Distribution */ asdf

2024-02-22T21:46:57Z

Distribution: asdf

← Older revision		Revision as of 21:46, 22 February 2024
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	= Distribution =		= Distribution =
	* put on DOCK license server		* put on DOCK license server
	* ~~details~~....		* copy dock3.8.x.tar.gz to dock server. test download and install
	* put on gimel		* put on gimel
	* ~~details ...~~		* same
	* put on wynton		* put on wynton
	* ~~details ...~~		* same
	* put in dockingorg/awsdock		* put in dockingorg/awsdock
	* ~~details ...~~		* bin and dock64

	= Testing at point of installation =		= Testing at point of installation =

Frodo: /* Get the 3D building pipeline */ asdf

2024-02-22T21:45:17Z

Get the 3D building pipeline: asdf

← Older revision		Revision as of 21:45, 22 February 2024
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	* mv zinc22-3d-submit zinc22-3d/bin		* mv zinc22-3d-submit zinc22-3d/bin
	* yeah, ok, this is funky, we will clean it up		* yeah, ok, this is funky, we will clean it up
			* git clone https://github.com/docking-org/SUBDOCK.git
			* mv SUBDOCK DOCK3.8/bin

	= Incorporate the fruits of (1), (2) and (3) into [[DOCK3.8]] repository housing an arsenal of scripts =		= Incorporate the fruits of (1), (2) and (3) into [[DOCK3.8]] repository housing an arsenal of scripts =

Frodo: /* Get the 3D building pipeline */ asdf

2024-02-22T21:40:55Z

Get the 3D building pipeline: asdf

← Older revision		Revision as of 21:40, 22 February 2024
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	* git clone https://github.com/docking-org/zinc22-3d.git		* git clone https://github.com/docking-org/zinc22-3d.git
	* instructions: https://wiki.docking.org/index.php/Building_The_3D_Pipeline_ZINC22		* instructions: https://wiki.docking.org/index.php/Building_The_3D_Pipeline_ZINC22
			* git clone https://github.com/docking-org/zinc22-3d-submit.git
			* mv zinc22-3d-submit zinc22-3d/bin
			* yeah, ok, this is funky, we will clean it up

	= Incorporate the fruits of (1), (2) and (3) into [[DOCK3.8]] repository housing an arsenal of scripts =		= Incorporate the fruits of (1), (2) and (3) into [[DOCK3.8]] repository housing an arsenal of scripts =

Frodo: /* Incorporate the fruits of (1), (2) and (3) into DOCK3.8 repository housing an arsenal of scripts */ asdf

2024-02-22T21:36:31Z

Incorporate the fruits of (1), (2) and (3) into DOCK3.8 repository housing an arsenal of scripts: asdf

← Older revision		Revision as of 21:36, 22 February 2024
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	* cp pydock3/dist/pydock3-0.1.0rc1-py3-none-any.whl DOCK3.8 # copy in pointer to scripts		* cp pydock3/dist/pydock3-0.1.0rc1-py3-none-any.whl DOCK3.8 # copy in pointer to scripts
	* cp dock3/src/i386/dock64 DOCK3.8 # copy in optimized executable		* cp dock3/src/i386/dock64 DOCK3.8 # copy in optimized executable
	* ~~cp -r~~ zinc22-3d ~~DOCK3~~.~~8 #~~ 3d ~~building pipeline~~		* tar czf DOCK3.8/zinc22-3d.tgz zinc22-3d
	* the release is now ready. create a tarball.		* the release is now ready. create a tarball.
	* tar czf dock_3.8.x.tar.gz DOCK3.8		* tar czf dock_3.8.x.tar.gz DOCK3.8

Frodo: asdf

2024-02-22T21:31:06Z

asdf

← Older revision		Revision as of 21:31, 22 February 2024
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	This page describes the formal definition of a release of the [https://dock.compbio.ucsf.edu/ ''UCSF DOCK''] software suite		This page describes the formal definition of a release of the [https://dock.compbio.ucsf.edu/ ''UCSF DOCK''] software suite

	1. Build [[pydock3]] Python package		= Build [[pydock3]] Python package =
	* (e.g., build pip-installable wheel file using [[Python Poetry\|poetry]]).		* (e.g., build pip-installable wheel file using [[Python Poetry\|poetry]]).
	* this can all be done on gimel2		* this can all be done on gimel2
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	* pip install dist/pydock3-0.1.0rc1-py3-none-any.whl		* pip install dist/pydock3-0.1.0rc1-py3-none-any.whl

	2. ~~Make a fresh and clean [[dock3]] executable~~		== (optional) create new python venv ==
			* https://wiki.docking.org/index.php/Create_venv

			= Make a fresh and clean [[dock3]] executable =
	* git clone https://github.com/docking-org/dock3.git		* git clone https://github.com/docking-org/dock3.git
	* ssh psi		* ssh psi
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	~~1A. (optional) create new python venv~~		= Get the 3D building pipeline =
	* https://wiki.docking.org/index.php/Create_venv

	3. Get the 3D building pipeline
	* git clone https://github.com/docking-org/zinc22-3d.git		* git clone https://github.com/docking-org/zinc22-3d.git
	* instructions: https://wiki.docking.org/index.php/Building_The_3D_Pipeline_ZINC22		* instructions: https://wiki.docking.org/index.php/Building_The_3D_Pipeline_ZINC22

	4. Incorporate the fruits of (1), (2) and (3) into [[DOCK3.8]] repository housing an arsenal of scripts (e.g., 3D build scripts, post-processing scripts) that are essential for following the [https://www.nature.com/articles/s41596-021-00597-z published Nature protocol].		= Incorporate the fruits of (1), (2) and (3) into [[DOCK3.8]] repository housing an arsenal of scripts =

			* (e.g., 3D build scripts, post-processing scripts) that are essential for following the [https://www.nature.com/articles/s41596-021-00597-z published Nature protocol].
	* mkdir DOCK3.8 # create an empty shell		* mkdir DOCK3.8 # create an empty shell
	* cp pydock3/dist/pydock3-0.1.0rc1-py3-none-any.whl DOCK3.8 # copy in pointer to scripts		* cp pydock3/dist/pydock3-0.1.0rc1-py3-none-any.whl DOCK3.8 # copy in pointer to scripts
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	* tar czf dock_3.8.x.tar.gz DOCK3.8		* tar czf dock_3.8.x.tar.gz DOCK3.8

	5. Distribution		= Distribution =
	* put on DOCK license server		* put on DOCK license server
	* details....		* details....
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	* details ...		* details ...

	6. Testing at point of installation		= Testing at point of installation =
	* test on DOCK license server (download, install, follow instructions)		* test on DOCK license server (download, install, follow instructions)
	* installation instructions....		* installation instructions....
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	* test on AWS		* test on AWS

	7. once tested, clean up old versions so the correct version to use is unambiguous.		= once tested, clean up old versions so the correct version to use is unambiguous. =

Frodo: asdf

2024-02-22T21:29:41Z

asdf

← Older revision		Revision as of 21:29, 22 February 2024
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	* git clone https://github.com/docking-org/pydock3.git		* git clone https://github.com/docking-org/pydock3.git
	* cd pydock3		* cd pydock3
	* git submodule update --init --recursive		* git submodule update --init --recursive. #why? dock3 is a submodule of pydock3. We need to tell git this.
	( you need to authenticate, and you need to have generated token)		( you need to authenticate, and you need to have generated token)
	* use the generated token as your password		* use the generated token as your password

Frodo: asdf

2024-02-22T21:25:07Z

asdf

← Older revision		Revision as of 21:25, 22 February 2024
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	5. Distribution		5. Distribution
	* put on DOCK license server		* put on DOCK license server
			* details....
	* put on gimel		* put on gimel
			* details ...
	* put on wynton		* put on wynton
			* details ...
	* put in dockingorg/awsdock		* put in dockingorg/awsdock
			* details ...

	6. Testing at point of installation		6. Testing at point of installation
	* test on DOCK license server (download, install, follow instructions)		* test on DOCK license server (download, install, follow instructions)
			* installation instructions....
	* test on gimel2		* test on gimel2
	* test on wynton		* test on wynton
	* test on AWS		* test on AWS

			7. once tested, clean up old versions so the correct version to use is unambiguous.

Frodo: asdf

2024-02-22T21:22:54Z

asdf

@@ Line 12: / Line 12: @@
 * ~isknight/.local/bin/poetry build
 * if there is a general python venv ready, use it. Else create new python venv (see below)
 * pip install dist/pydock3-0.1.0rc1-py3-none-any.whl
@@ Line 30: / Line 31: @@
 A. (optional) create new python venv
 A particular commit of the DOCK3.8 repository formally becomes a particular distribution of [https://dock.compbio.ucsf.edu/ ''UCSF DOCK''] software when the commit is tagged with the distribution's [https://semver.org/ semantic version (e.g., DOCK3.8 v1.2.0)]. Note that ''pydock3'' and ''dock3'' are separately versioned from ''DOCK3.8''.

Frodo: asdf

2024-02-22T21:00:39Z

asdf

← Older revision		Revision as of 21:00, 22 February 2024
Line 1:		Line 1:
	This page describes the formal definition of a release of the [https://dock.compbio.ucsf.edu/ ''UCSF DOCK''] software suite		This page describes the formal definition of a release of the [https://dock.compbio.ucsf.edu/ ''UCSF DOCK''] software suite

	1. Build ~~desired version of~~ [[pydock3]] Python package (e.g., build pip-installable wheel file using [[Python Poetry\|poetry]]).		1. Build [[pydock3]] Python package
			* (e.g., build pip-installable wheel file using [[Python Poetry\|poetry]]).
	* this can all be done on gimel2		* this can all be done on gimel2
	* git clone https://github.com/docking-org/pydock3.git		* git clone https://github.com/docking-org/pydock3.git
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	* run poetry, e.g.		* run poetry, e.g.
	* ~isknight/.local/bin/poetry build		* ~isknight/.local/bin/poetry build
			* if there is a general python venv ready, use it. Else create new python venv (see below)
	* pip install dist/pydock3-0.1.0rc1-py3-none-any.whl		* pip install dist/pydock3-0.1.0rc1-py3-none-any.whl

	2. ~~Clone desired version of~~ [[dock3]] ~~program.~~		2. Make a fresh and clean [[dock3]] executable

	* git clone https://github.com/docking-org/dock3.git		* git clone https://github.com/docking-org/dock3.git
	* ssh psi		* ssh psi
			* bash
			* export PATH=/nfs/soft/pgi/current/linux86-64/12.10/bin:$PATH
			* source /nfs/home/tbalius/zzz.virtualenvs/virtualenv-1.9.1/myVEonGimel/bin/activate
			* source /nfs/soft/pgi/env.sh
			* verify that compiler set to pgf95 in Makefiles
			* cd into libfgz
			* make clean; make
			* cd into i386
			* make clean; make


			1A. (optional) create new python venv