Blastermaster2.0: Difference between revisions
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== All others == | == All others == | ||
=== 0. Copy the | === 0. Copy the relevant files 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). | Copy your rec.pdb and xtal-lig.pdb files to your directory. If you want to provide your own rec.crg.pdb, copy that in too. 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 === | === 1. Generate a blaster config file to your directory === | ||
Revision as of 18:32, 8 April 2022
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 relevant files to your directory
Copy your rec.pdb and xtal-lig.pdb files to your directory. If you want to provide your own rec.crg.pdb, copy that in too. 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>
2. Edit the blaster config file to your specifications
3. Crucially, set an environmental variable called `DOCKBASE` to the path of your DOCK software directory.
export DOCKBASE=<ABSOLUTE_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.