Blastermaster2.0: Difference between revisions

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[deprecated]


= Installation =
See [[blastermaster (pydock3 script)]]
 
== System dependencies ==
 
You will need CSH to run .csh files.
 
E.g., on Ubuntu 20:
sudo apt-get install csh
 
At least some of the blaster programs that BM2 depends on are 32-bit, so '''if you are installing on a 64-bit architecture then you will need to enable 32-bit architecture and install the relevant libraries'''
 
E.g., on Ubuntu 20:
sudo dpkg --add-architecture i386
sudo apt-get update -y
sudo apt-get install libc6:i386 libncurses5:i386 libstdc++6:i386
 
E.g., on CentOS 7:
yum install glibc.i686 libstdc++.i686
 
== Installing using Pip ==
 
Assuming you have a valid [https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token GitHub personal access token (PAT)] attached to a GitHub account that has read-access to [https://github.com/docking-org/blastermaster-2.0 Blastermaster 2.0 repository within the Docking.org GitHub organization], you can install BM2 to a given Python environment using Pip:
 
pip install https://<GIT_ACCESS_TOKEN>@raw.githubusercontent.com/docking-org/blastermaster-2.0/main/dist/bm2-0.1.0-py3-none-any.whl
 
= Using Blastermaster 2.0 =
 
== UCSF Shoichet Lab members ==
 
If you are a member of the UCSF Shoichet Lab, you can use BM2 on one of the UCSF computers where it is already set-up. See here: [[How_to_use_Blastermaster_2.0_on_UCSF_computers|https://wiki.docking.org/index.php/How_to_use_Blastermaster_2.0_on_UCSF_computers]]
 
== All others ==
 
=== 0. Copy the blaster config file to your directory ===
Copy your rec.pdb and xtal-lig.pdb files to your directory. Blastermaster 2.0 will look for these in the directory in which you run it.
 
=== 1. Generate a blaster config file to your directory ===
The following will generate a file called "blasterconfig.yaml"
blasterconfig
The following will generate a file called whatever you put for <BLASTER_CONFIG_FILE_NAME>
blasterconfig <BLASTER_CONFIG_FILE_NAME>
 
=== 2. Edit the blaster config file to your specifications ===
Crucially, set an environmental variable called `DOCKBASE` to the path of your DOCK software directory.
=== 3. Run ===
blastermaster <BLASTER_CONFIG_FILE_NAME>
 
= Tips for users =
 
You can create and save multiple blaster config files with different settings so long as they have different names (e.g. blasterconfig_default.yaml, blasterconfig_use_existing_charged_receptor.yaml). Then it is easy to reuse the same configuration settings at a later time.
 
 
[[Category:blastermaster2.0]]
[[Category:active_development]]

Latest revision as of 08:16, 2 September 2022

[deprecated]

See blastermaster (pydock3 script)

Retrieved from "http://wiki.docking.org/index.php?title=Blastermaster2.0&oldid=14746"