How to install DOCK 3.8: Difference between revisions

From DISI
Jump to navigation Jump to search
m (asdf)
 
(7 intermediate revisions by 2 users not shown)
Line 1: Line 1:
== Installation/Download ==
Many of the tutorials on how to use DOCK software assume you have access to an executable DOCK program- sometimes referred to as DOCKEXEC, or simply DOCK. This page describes how to gain access to this program.


These instructions are only for developers. To install DOCK 3.8 for non-developers, please obtain a license via the DOCK license server [https://dock.docking.org/Online_Licensing/dock_license_application.html | dock.compbio.ucsf.edu] and download the software.
== Obtaining a License ==


The up-to-date docking scripts for DOCK 3.8 are hosted primarily on github. https://github.com/docking-org/DOCK/tree/dev
Please obtain a license via the DOCK license server [[https://dock.docking.org/Online_Licensing/dock_license_application.html]] and download the software.


If you already have a docking-org repository cloned to your machine, simply do the following:
== Compiling from source ==


  <nowiki>
See this page: [[How_to_compile_DOCK]]
git pull
 
cd DOCK
If you are a BKS cluster member, you should follow the instructions for compiling via pgf. The DOCK 3.8 source can be found on github:
DOCKBASE=$PWD</nowiki>
 
  <nowiki>git clone https://github.com/docking-org/dock3.git</nowiki>
 
For any others without a PGF license, follow the gfortran instructions.
 
== Prebuilt Executable ==


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 (which is world-writable):


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
dock38_nogist    : DOCK 3.8 sans error messages that sometimes occur when using recently built ligand libraries</nowiki>


If you're on BKS, you can find DOCK 3.8 @ /nfs/soft/dock/versions/dock38/DOCK-current
You are encouraged to also included the source code in this directory as a tar.gz file with the same base name as your executable.


<nowiki>
DOCKBASE=/nfs/soft/dock/versions/dock38/DOCK-current</nowiki>


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

Latest revision as of 04:52, 3 March 2023

Many of the tutorials on how to use DOCK software assume you have access to an executable DOCK program- sometimes referred to as DOCKEXEC, or simply DOCK. This page describes how to gain access to this program.

Obtaining a License

Please obtain a license via the DOCK license server [[1]] and download the software.

Compiling from source

See this page: How_to_compile_DOCK

If you are a BKS 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 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 (which is world-writable):

/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 ligand libraries

You are encouraged to also included the source code in this directory as a tar.gz file with the same base name as your executable.