zenglab_server

This is PKU ZengHu‘s lab server wiki repository This wiki references the laboratory management manual by StatBiomed For lab member use:

• Current LAN IP in PKU http://10.128.243.62/
• this is a dynamic address, which means it may change after reboot

Login, account data management

This part is important, please see instructions in the SSH&DataManagement.md page

Environment with Conda

Installing anaconda ,miniconda, mamba yourself to create base environment for your own. But for specific task, create your own conda environment, so that you can control all versions of the packages for your analysis, which is important for reproducibility. Follow the conda manual to manage your environments. For pipeline (such as Snakemake) or software you create for your own ,leave a copy on public Conda or wet lab team can access to them easily

For each environment, you can also add it as a separated kernel on jupyter lab, see here:

conda activate myenv

pip install ipykernel

python -m ipykernel install --user --name myenv --display-name "Python (myenv)"

For public conda ,your can source and activate via

source /media/zenglab/miniconda3/etc/profile.d/conda.sh 
conda activate publiccenv

VS Code

• See instructions on the Vscode page

Jupyterlab on server

• Directly available (http not https): http://10.128.243.62:8000
• See instructions on the [Jupyter.md](https://github.com/ZenghuPKU/zenglab_server/blob/main/Jupyter.md
• )(To be continued)

RStudio server

• Directly available (http not https): http://10.128.243.62:8787
• See instructions on the R.md page (To be continued)