Quick Reference

Essential BioGrids commands and configurations.

Environment Setup

Initialize the BioGrids environment with source /programs/biogrids.shrc for Bash or source /programs/biogrids.cshrc for Tcsh.

For automatic loading, add the source command to your shell configuration file (~/.bashrc for Bash, ~/.tcshrc for Tcsh). Create an alias like alias sbg='source /programs/biogrids.shrc' for on-demand activation.

BioGrids CLI Commands

Common Commands

Manage software with biogrids-cli list, biogrids-cli install package, biogrids-cli installed, and biogrids-cli remove package. Check system status with biogrids-cli check-connection and biogrids-cli verify. Search packages with biogrids-cli search keyword and get details with biogrids-cli info package.

GPU Computing

Check GPU status with nvidia-smi and CUDA version with nvcc --version. Install GPU software using package names with _gpu or _cuda suffixes. List GPU packages with biogrids-cli list --gpu-only. Control GPU visibility with export CUDA_VISIBLE_DEVICES=0,1.

Example Workflow

For RNA-seq analysis, install tools with biogrids-cli install fastqc trimmomatic samtools star subread, then activate the environment with source /programs/biogrids.shrc. Check R package availability by loading it in R with library(packagename).

Troubleshooting

Verify BioGrids activation with ls /programs/ and check environment with echo $BIOGRIDS_ROOT. Test network connectivity with curl -I http://portquiz.net:873. Reset the environment with source /programs/biogrids.shrc.

Admin operations include biogrids-cli admin for maintenance, biogrids-cli rebuild for environment refresh, and biogrids-cli crontab for scheduled tasks.

File Locations

Main installation is at /programs with configuration files biogrids.shrc and biogrids.cshrc. Personal settings are in ~/.biogrids.conf.

For help, use biogrids-cli help <command> or contact help@biogrids.org.