readme

In this directory code snippets are organized in separate markdown files based on software, task, etc.

The Wiki for this repo contains more detailed guides and instructions on things like:

• Jupyter Notebooks.
  • Jupyter Notebooks are an ideal means to document (and improve reproducibility) of computing commands.
• Super Computing with Mox (hyak)
  • Mox is a high powered designed computer designed for seriously intensive computing
  • Due to the steep learning curve, it has its own dedicated wiki.
• Docker
  • Docker is a means to run a virtual Linux computer (great for Windows users!).
  • We have as Docker setup to install the most commonly used software used in the Roberts Lab, including Jupyter Notebook.

---

File Descriptions

• R.md - Intended for R tips. Currently empty.

• README.md - This is the file you're currently reading.

• bash.md - Collection of commonly used bash commands for counting, finding & replacing, and moving/renaming files.

• fasta.md - FASTA file manipulation including counting sequences, converting FASTQ to FASTA, & converting FASTA to tab-delmited.

• jupyter.md - Ways to work with Jupyter Notebooks including embedding notebooks in websites, viewing notebooks on nbviwer.com, and using Jupyter Notebooks on remote computers.

• misc.md - Tips for using SSH, MD5 checksums, and gzip manipulation.

• nf_core-base-srlab-500GB-node.config: Nextflow config file for use with Roberts Lab 500GB Mox computing node.

• remote_connections.md - Ways to connect to computers remotely (via SSH), how to create/use SSH keys, create tunnels, and tmux to keep jobs running after closing SSH sessions.

• snippets.cson: Atom text editor snippets file which allows for autocompletion of markdown-formatted text frequently used by Roberts Lab members when writing in markdown (e.g. in notebooks). This file can be copied to ~/.atom/ on your computer for use and will overwrite the default snippets file.

• sqlshare.md - Tips for using SQLshare, but most commands are compatible with MySQL and/or SQLite. Lots of tips on joining tables and counting values.

• vscode-snippets.code-snippets: Visual Studio Code global snippets file which allows for autocompletion of markdown-formatted text frequently used by Roberts Lab members when writing in markdown (e.g. in notebooks). This file can be copied to ~/.config/Code/User/snippets/vscode-snippets.code-snippets on your computer for use and will overwrite the default snippets file.