Skip to content

Installation of bedder

Binary options

  • bedder-static-linux-x86_64: Static binary for Linux x86_64
  • bedder-static-macos-x86_64: Mostly static binary for macOS x86_64

Linux Installation

As of June 2025, the linux binary, when installed on a cluster, requires the use of a python virtual environment (venv). 

# Download Linux binary and make it executable
wget https://github.com/quinlan-lab/bedder-rs/releases/download/v0.1.2/bedder-static-linux-x86_64
chmod +x bedder-static-linux-x86_64

# Check whether install was successful
./bedder-static-linux-x86_64
If installation is successful, running the command "bedder" should produce an error regarding lack of input arguments: 
[<DATE> INFO  bedder] starting up
error: the following required arguments were not provided:
  -a <QUERY_PATH>
  -b <OTHER_PATHS>
  --genome <GENOME_FILE>

Linux troubleshoot

If installation is unsuccessful, consider:

Reinstalling in a python virtual environment

python -m venv venv
source venv/bin/activate
wget https://github.com/quinlan-lab/bedder-rs/releases/download/v0.1.2/bedder-static-linux-x86_64
chmod +x bedder-static-linux-x86_64

Calling the command from the current directory

./bedder-static-linux-x86_64

Relocating the binary to $PATH

This may be necessary if above check fails or if you are hoping to install the linux binary in a particular location distinct from the default. 

# To determine what $PATH are available: 
echo "$PATH"
# Move to $PATH
sudo mv bedder-static-linux-x86_64 /usr/local/bin/bedder

macOS Installation

# Download Mac binary and make executable
wget https://github.com/quinlan-lab/bedder-rs/releases/download/v0.1.2/bedder-static-macos-x86_64
chmod +x bedder-static-macos-x86_64

# Check whether install was successful
./bedder-static-macos-x86_64
Once again, if installation is successful, running the command "bedder" should produce the following error regarding lack of input arguments: 
[<DATE> INFO  bedder] starting up
error: the following required arguments were not provided:
  -a <QUERY_PATH>
  -b <OTHER_PATHS>
  --genome <GENOME_FILE>

macOS troubleshoot

If installation is unsuccessful, consider:

Reinstalling in a python virtual environment

python -m venv venv
source venv/bin/activate
wget https://github.com/quinlan-lab/bedder-rs/releases/download/v0.1.2/bedder-static-macos-x86_64
chmod +x bedder-static-macos-x86_64

Calling the command from the current directory

./bedder-static-macos-x86_64

Relocating the binary to $PATH

This may be necessary if above check fails or if you are hoping to install the macOS binary in a particular location distinct from the default. 

# To determine what $PATH are available: 
echo "$PATH"
# Move to $PATH
sudo mv bedder-static-macos-x86_64 /usr/local/bin/bedder

Binary Information

  • Linux binary: Fully static (~6MB, no dependencies)
    • fully static when installing on a local machine
    • testing has identified that as of June 2025, installation on a remote cluster may require the use of a python venv
  • macOS binary: Mostly static (~6MB, minimal system dependencies)
  • Python: Works with any Python 3.8+ system
  • Architecture: x86_64