Cheat sheets¶

On this page we collected a set of notes used for quick reference.

Apocrita / Andrena cheat sheet¶

Job submission / Information¶

Command	Description
`qsub jobscript.sh`	Submits job script jobscript.sh to the queue (man qsub)
`qstat -j jobnumber`	Shows information about job jobnumber
`qhold jobnumber`	Apply a hold on job jobnumber - jobs is held from running (qhold)
`qsub -hold_jid jobscript.sh`	Submits job script jobscript.sh and apply hold (qhold)
`qrls jobnumber`	Releases job for execution (removes hold) (qhold)
`qdel jobnumber`	Deletes running/queued job jobnumber (man qdel)
`jobstats`	Show details of completed cluster jobs (jobstats)
`qacct -j jobnumber`	Report and account for job usage (man qacct)
`qmquota`	Displays your current storage quotas and usage (qmquota)

Queues / Nodes¶

Command	Description
`qstat`	Show the status of submitted cluster jobs (man qstat)
`showqueue`	Show details of submitted jobs waiting to run (showqueue)
`showqueue -F`	Show details of submitted jobs waiting to run, with additional information (showqueue)
`nodestatus`	Shows the status of the cluster nodes (nodestatus)

Modules¶

Command	Description
`module avail`	Show the available modules on the cluster
`module list`	Show loaded modules in the current environment
`module load modulename`	Loads module modulename e.g. `module load python`
`module switch moduleversion`	Switch version of previously loaded module to moduleversion e.g. `module switch python`
`module unload modulename`	Unload a specific loaded module e.g. `module unload python`
`module purge`	Unload all loaded modules

Linux commands cheat sheet¶

Basic commands¶

Command	Description
`man command`	Show manual for command

Directory Operations¶

Command	Description
`pwd`	Show current directory
`mkdir dir`	Create directory dir
`cd dir`	Change directory to dir
`ls`	List directory contents

File Operations¶

Command	Description
`cat file1 file2`	Print the contents of files file1 and file2 to the stdout
`less file1`	Display the contents of file1 in a paginated form
`file file1`	Display the file type of object file1
`cp file1 file2`	Copy file1 to file2
`mv file1 file2`	Move (or rename) file1 to file2
`rm file1`	Delete file1
`head file1`	Show first 10 (default) lines of file1
`tail file1`	Show last 10 (default) lines of file1
`tail -f file1`	Output appended data as file1 grows

File Permissions¶

Command	Description
`chmod 755 file`	Change mode of file to 755 (`rwxr-xr-x`)
`chmod -R 600 directory`	Recursively change access mode of directory to 600 (`rw-------`)
`chown user:group file`	Change file owner to user and group to group

Process Management¶

Command	Description
`ps`	Show snapshot of processes
`top`	Show real time processes
`kill pid`	Kill process with id pid

Bash Shortcuts¶

Shortcut	Description
`CTRL + c`	Stop current command
`CTRL + r`	Search history
`!!`	Repeat last command

See the Linux cheat sheet for more Linux commands.

GIT cheat sheet¶

Git basics¶

Command	Description
`git init`	Create an empty Git repo in the specified directory.
`git clone repo`	Clone repo located at repo onto local machine.
`git config user.name name`	Define author name to be used for all commits in the current repo.
`git add directory`	Stage all changes in directory for the next commit. Replace directory with a file to change a specific file.
`git commit -m "message"`	Commit the staged snapshot using message as the commit message
`git status`	List which files are staged, unstaged, and untracked.
`git log`	Display the entire commit history using the default format.
`git pull`	Fetch remote’s copy of current branch and merge it into the local copy.
`git pull --rebase remote`	Fetch the remote’s copy of current branch and rebase it into the local copy.
`git push remote branch`	Push the branch to remote, along with the necessary commits and objects.
`git push remote --force`	Forces the git push even if it results in a non-fast-forward merge.

Git branches¶

Command	Description
`git branch`	List all of the branches in your repo.
`git checkout branch`	Check out an existing branch named branch.
`git checkout -b branch`	Create and check out a new branch named branch.

See the Git cheat sheet for more Git commands.

Anaconda / Mamba / Miniconda cheat sheet¶

Tips and recommendations¶

It is recommended to create a new environment for any new project or workflow.
Package dependencies and platform specifics are automatically resolved when using conda.
When importing an environment, conda resolves platform and package specifics.
Specifying the environment name confines conda commands to that environment.
Name the export file "environment". Environment name will be preserved.

Quick start¶

Command	Description
`conda info`	Verify conda install and check version
`conda create --name ENVNAME`	create a new environment with name ENVNAME (tip: name environment descriptively)
`conda activate ENVNAME`	activate environment ENVNAME (do this before installing packages)

Working with conda environments¶

Command	Description
`conda env list`	list all environments and locations
`conda list -n ENVNAME --show-channel-urls`	list all packages + source channels in ENVNAME
`conda install -n ENVNAME PKG1 PKG2`	install packages PKG1 PKG2 in environment ENVNAME
`conda uninstall PKGNAME -n ENVNAME`	remove package PKGNAME from environment ENVNAME
`conda update --all -n ENVNAME`	update all packages in environment ENVNAME

Environment management¶

Command	Description
`conda create -n ENVNAME python=3.10`	create environment ENVNAME with Python version 3.10
`conda remove -n ENVNAME --all`	delete environment by name
`conda list -n ENVNAME --revisions`	list revisions made to environment ENVNAME

Importing environments¶

Command	Description
`conda env create -n ENVNAME --file ENVNAME.yml`	Create environment ENVNAME from a ENVNAME.yml file
`conda create -n ENVNAME --file ENVNAME.txt`	Create environment ENVNAME from a ENVNAME.txt file

Exporting environments¶

Command	Description
`conda env export --from-history>ENVNAME.yml`	cross-platform compatible
`conda env export ENVNAME>ENVNAME.yml`	platform + package specific
`conda list --explicit>ENVNAME.txt`	platform + package + channel specific

Channels and packages¶

Command	Description
`conda list`	list installed packages
`conda update --all`	update all packages
`conda install -c CHANNELNAME PKG1 PKG2`	install packages PKG1 PKG2 from specific channel CHANNELNAME
`conda install PKGNAME=3.1.4`	install specific version 3.1.4 of package PKGNAME
`conda install CHANNELNAME::PKGNAME`	install a package PKGNAME from specific channel CHANNELNAME
`conda uninstall PKGNAME`	uninstall package PKGNAME
`conda config --add channels CHANNELNAME`	add channel CHANNELNAME

Additional hints¶

Command	Description
`conda COMMAND --help`	get help for command COMMAND
`conda search PKGNAME --info`	get info for package PKGNAME
`conda install PKG1 PKG2 --yes`	run commands w/o user prompt e.g., installing multiple packages
`conda clean --all`	remove all unused files
`conda config --show`	examine conda configuration

See the Anaconda cheat sheet for more Anaconda commands.

Vi / Vim cheat sheet¶

Exiting¶

Command	Description
`:q`	Close file
`:q!`	Close without saving
`:w`	Save
`:wq`	Save and close file
`:x`	Save and close file

Clipboard¶

Command	Description
`x`	Delete character
`dd`	Delete line (Cut)
`yy`	Yank line (Copy)
`p`	Paste
`P`	Paste before

Editing¶

Command	Description
`a`	Append
`i`	Insert
`u`	Undo changes
`Esc`	Exit insert mode

Operators list¶

Command	Description
`d`	Delete
`y`	Yank (copy)
`c`	Change (delete then insert)

See the Vim cheat sheet for more Vim commands.