Blastermaster2.0

Installation

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 GitHub personal access token (PAT) attached to a GitHub account that has read-access to 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-<SEMANTIC_VERSION>-py3-none-any.whl

where <GIT_ACCESS_TOKEN> and <SEMANTIC_VERSION> are replaced by their corresponding / desired values. E.g. semantic version: 0.1.0

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: 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 (or at whichever file paths you set for their corresponding parameters in the config file).

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>

3. Crucially, set an environmental variable called `DOCKBASE` to the path of your DOCK software directory.

export DOCKBASE=<PATH_TO_DOCK_REPOSITORY>

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.