# Intro to Unix

###### tags: `code`

## Shells

You use a shell (we're using bash) to interact with an operating system. We are using Linux, Ubuntu (particular flavor of Unix)
## File System Organization
- organizes your work into folders
- several layers of 'nested' folders, you often have to think relative to yourself when working in the directory
- folder navigation always relative to the current directory
## Commands
All commands have the following format:
VCM:~$ command parameters outputs

Good commands:

Up and down arrows will show you previous commands you've typed before

- `cd` = change directory
1) `.` -> stays same place
2) `..` -> moves you one step up parent directory
3) `../..` -> moves you two steps up to even bigger parent directory
4) `subdirectory/` hit tab key twice and will show possibilities
5) if you just type `cd` with nothing else, it will take you home

- `mkdir`
- `rmdir`
- `cp` = copy
- `mv` = move
- `rm` = remove
- `gzip` = decompress (ex. `gzip -d dmel-all-tRNA-r6.45.fasta.gz`)
- `scp` = secure copy
- echo "test" > textme.txt
- now login to wherever you want to move the file to:
- scp -i .ssh/IDKEY labuser@34.148.164.14:~testme.txt
- `sftp` = secure transfer file
- `wget` = grabbing stuff from online

## Conda Environment
- conda is a software tool for managering installed software. You create an environment for whatever you are working on.

conda info --envs

We're using BioInfo Conda environment

conda info bioinfo

to get out you can type `conda deactivate`

conda list

will tell you everything in this conda environment

conda create -n myblast
conda activate myblast

Threads = way to specify how many working units at once? Each CPU can use 2 threads; Each CPU core can have two threads. So a processor with two cores will have four threads. A processor with eight cores will have 16 threads.

`-t #of threads`