DOCK 3.8:How to build a release: Difference between revisions

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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 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
Line 10: Line 11:
* 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




Revision as of 21:00, 22 February 2024

This page describes the formal definition of a release of the UCSF DOCK software suite

1. Build pydock3 Python package

( you need to authenticate, and you need to have generated token)

  • use the generated token as your password
  • run poetry, e.g.
  • ~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

2. Make a fresh and clean dock3 executable

  • git clone https://github.com/docking-org/dock3.git
  • 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


3. Incorporate the fruits of (1) and (2) into DOCK3.8 repository housing an arsenal of scripts (e.g., 3D build scripts, post-processing scripts) that are essential for following the published Nature protocol.

A particular commit of the DOCK3.8 repository formally becomes a particular distribution of UCSF DOCK software when the commit is tagged with the distribution's semantic version (e.g., DOCK3.8 v1.2.0). Note that pydock3 and dock3 are separately versioned from DOCK3.8.

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