How to install DOCK 3.8: Difference between revisions

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== install ==
== Compiling from source ==
* get a computer
* go to dock.compbio.ucsf.edu. get a license.
[https://dock.docking.org/Online_Licensing/dock_license_application.html dock.compbio.ucsf.edu]


* download tarball
See this page: [[How_to_compile_DOCK]]
* unpack tarball:   tar xzf dock.3.8_source.tar.gz
you now have a directory pydock3-0.1.0 (or so)


* make sure you have python 3.8 or later.
If you are a BKS or Wynton cluster member, you should follow the instructions for compiling via pgf. The DOCK 3.8 source can be found on github:
* bash
* source /nfs/soft/python/python3.8.5.sh
* (some command to install)


== access for developers ==
  <nowiki>git clone https://github.com/docking-org/dock3.git</nowiki>


* https://github.com/docking-org/pydock3
For any others without access to our clusters or a PGF license, follow the gfortran instructions.


<nowiki>
== Prebuilt Executable ==
git clone https://github.com/docking-org/pydock3
cd DOCK
DOCKBASE=$PWD</nowiki>


And retrieve the scripts from DOCK/docking/submit/sge and DOCK/docking/submit/slurm.
DOCK is constantly being modified & fine-tuned, sometimes there may be a special version of DOCK floating around you want to use, or perhaps you have a special version of your own you'd like to share. We collect all custom DOCK executables on the BKS cluster at this location:


If you don't have the repository already cloned to your machine, you just need to clone it first:
<nowiki>/nfs/soft/dock/versions/dock38/executables</nowiki>


Here is a brief description of the various executables here at the time of writing:
  <nowiki>
  <nowiki>
git clone https://github.com/docking-org/DOCK.git
dock37_vanilla  : standard DOCK 3.7 executable
cd DOCK
dock38_vanilla  : standard DOCK 3.8 executable
DOCKBASE=$PWD</nowiki>
dock37_matchcap  : DOCK 3.7 executable that more strictly caps the number of matches DOCK generates - slightly faster!
 
dock38_matchcap : Same as above, but for 3.8
If you're on BKS, you can find DOCK 3.8 @ /nfs/soft/dock/versions/dock38/DOCK-current
dock38_nogist    : DOCK 3.8 sans error messages that sometimes occur when using recently built libraries</nowiki>
 
  <nowiki>
DOCKBASE=/nfs/soft/dock/versions/dock38/DOCK-current</nowiki>
 




[[Category:DOCK 3.8]]
[[Category:DOCK 3.8]]
[[Category:Developers]]
[[Category:Developers]]

Revision as of 20:54, 2 March 2023

Compiling from source

See this page: How_to_compile_DOCK

If you are a BKS or Wynton cluster member, you should follow the instructions for compiling via pgf. The DOCK 3.8 source can be found on github: 

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

For any others without access to our clusters or a PGF license, follow the gfortran instructions.

Prebuilt Executable

DOCK is constantly being modified & fine-tuned, sometimes there may be a special version of DOCK floating around you want to use, or perhaps you have a special version of your own you'd like to share. We collect all custom DOCK executables on the BKS cluster at this location: 

/nfs/soft/dock/versions/dock38/executables

Here is a brief description of the various executables here at the time of writing: 

dock37_vanilla   : standard DOCK 3.7 executable
dock38_vanilla   : standard DOCK 3.8 executable 
dock37_matchcap  : DOCK 3.7 executable that more strictly caps the number of matches DOCK generates - slightly faster!
dock38_matchcap  : Same as above, but for 3.8
dock38_nogist    : DOCK 3.8 sans error messages that sometimes occur when using recently built libraries
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