BGEN¶
A suite of tools to analyse binary GEN files.
Conda installation¶
BGEN can be installed from the Conda Forge Anaconda channel by loading the Miniforge module and then creating a Conda environment and installing BGEN into it (output below truncated):
$ module load miniforge
$ mamba create --quiet --yes --name bgen_env
$ mamba activate bgen_env
(bgen_env) $ mamba install conda-forge::bgenix
Looking for: ['conda-forge::bgenix']
...
Updating specs:
- conda-forge::bgenix
...
Confirm changes: [Y/n] Y
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Usage¶
To run the Conda installed version of BGEN, simply load the miniforge module
and activate the Conda environment you installed it into:
$ module load miniforge
$ mamba activate bgen_env
(bgen_env) $ bgenix -help
Usage: bgenix <options>
For usage documentation, run bgenix -help.
The BGEN suite contains single threaded applications
All tools in the BGEN suite do not provide support for multi-threading so please only request 1 core in your submission scripts. Any additional cores requested will be unused and wasted.
Example job¶
Serial job¶
Here is an example job running on 1 core and 1GB of memory to build an index for the specified BGEN file:
#!/bin/bash
#SBATCH --ntasks=1 # (or -n 1) Request 1 core
#SBATCH --mem-per-cpu=1G # Request 1GB RAM per core (1GB total)
#SBATCH --time=1:0:0 # (or -t 1:0:0) Request 1 hour runtime
module load miniforge
mamba activate bgen_env
bgenix -g example.bgen -index