computing_tips.md

Computing tips

Running jobs in the background

• Running jobs in the background with screen. [Anyone add some links or texts?]

IDE: PyCharm, VS Code, and Jupyter lab

Huang lab notes

• See PBS.md for submitting tasks to PBS system and using conda with PBS.
• See plotting.md for tips on plotting with publication standard.

Linux useful commands

• Downloading large files from clouds (Google Drive, OneDrive) or data repositories with wget
• ctrl + Z, followed by kill %% to kill previous job [add links?]

Conda environment directory

• Change the configuration setting
• Add jupyter kernel with ipykernel

SRA/fastq at EBI database

• Ruiyan add more links

Misc

• Python module auto reload [links ?]
• Using VS Codes on cluster (Weizhong's note) and Jupyter on cluser (jupyte tips)
• Excel Table to Latex table (google sheet adds-on, or using R)