/linux-cheat-sheet

General

  • mkdir -p folder/subfolder - Inculde creation of parent dir
  • tail -f - Monitor a log file
  • ls -lah - List files with better information
  • du -h -d1 - List top level directory space usage
  • srun --ntasks=1 --cpus-per-task=1 --partition=int --time=4:00:0 --mem=4G --pty /bin/bash - Create interactive node on CAMP
  • pwd - Show current path
  • whoami - Current login username
  • tree - Tree directory structure
  • ln -s <source> <dest> - Symbolic link
  • find ./myfolder -mindepth 1 ! -regex '^./myfolder/test2\(/.*\)?' -delete - this will delete all folders inside ./myfolder except that ./myfolder/test2 and all its contents will be preserved

Screen

  • screen -S nextflow -m bash -c 'sh run.sh; exec sh' - Run named screen session with wait command at end so window doesnt auto-close
  • screen -ls - List screens
  • screen -r 344074 - Attatch to running screen with number before decimal point
  • screen -X -S [session # you want to kill] quit - kill session
  • Screen ctrl+a+d detatch

macos

  • sudo nano /etc/paths - Edit path on mac

Nextflow

  • nextflow run <REPO> - Runs pipeline from github
  • nextflow pull <REPO> - Updates repo from github
  • nextflow run <SCRIPT> -w <WORKDIR> - Specify work dir
  • nextflow run <SCRIPT> -ansi-log false - Change log to each task (good for debugging)
  • singularity pull --name <NAME>.img docker://<PATH>:<TAG> > /<TAG>/null - Pull custom docker image
  • rm -rf ~/.nextflow/assets/<REPO-PATH> - Removes downloaded repo if switching branches etc
  • rm -rf .nextflow* results work - Clean a working directory if having problems

Containers

Vagrant

Creating a VM

  • vagrant init -- Initialize Vagrant with a Vagrantfile and ./.vagrant directory, using no specified base image. Before you can do vagrant up, you'll need to specify a base image in the Vagrantfile.
  • vagrant init <boxpath> -- Initialize Vagrant with a specific box. To find a box, go to the public Vagrant box catalog. When you find one you like, just replace it's name with boxpath. For example, vagrant init ubuntu/trusty64.

Starting a VM

  • vagrant up -- starts vagrant environment (also provisions only on the FIRST vagrant up)
  • vagrant resume -- resume a suspended machine (vagrant up works just fine for this as well)
  • vagrant provision -- forces reprovisioning of the vagrant machine
  • vagrant reload -- restarts vagrant machine, loads new Vagrantfile configuration
  • vagrant reload --provision -- restart the virtual machine and force provisioning

Getting into a VM

  • vagrant ssh -- connects to machine via SSH
  • vagrant ssh <boxname> -- If you give your box a name in your Vagrantfile, you can ssh into it with boxname. Works from any directory.

Stopping a VM

  • vagrant halt -- stops the vagrant machine
  • vagrant suspend -- suspends a virtual machine (remembers state)

Cleaning Up a VM

  • vagrant destroy -- stops and deletes all traces of the vagrant machine
  • vagrant destroy -f -- same as above, without confirmation

Docker

  • docker build -t <CONTAINER>:<TAG> <FOLDER CONTAINING DOCKERFILE> -- build new image from docker file
  • docker images -- View local images
  • docker run -it <CONTAINER>:<TAG> /bin/bash -- Run a container with an interactive shell
  • docker push <CONTAINER>:<TAG> -- Pushes local image to docker hub
  • docker image prune -- By default, docker image prune only cleans up dangling images. A dangling image is one that is not tagged and is not referenced by any container.
  • docker image prune -a --To remove all images which are not used by existing containers, use the -a flag:
  • docker image rm <CONTAINER_ID> -- Remove specific image