Week 1 cheatsheet
Programming with Python (for Bioinformatics)
Jens Zentgraf, Johanna Schmitz
Winter 2022/23
Basic Bash Commands
• Absolute vs. relative path
– Current folder is your home folder
– Downloads folder:
∗ Relative path: Downloads
∗ Absolute path: /home/username/Downloads
– ~ is an alias for /home/username
• Change directory cd:
– cd or cd ~: Switch to your home folder
– cd ..: Switch to parent directory
– cd ../..: Go up two directories
– cd Downloads: Switch into the Downloads
folder
You can use a relative or absolute path
– cd -: Switch to the last directory
• Move/rename a file mv:
– mv file target_path: Moves file to the tar-
get folder
Git Commands
Clone Course Repository
1. Create GitLab account: https://gitlab.com/users/s
ign_in
2. Add ssh key to your GitLab account
1. If you don’t have an ssh key on your machine
(in ~/.ssh folder)
• open a terminal
• generate ssh key using the command
ssh-keygen -t ed25519
• press enter to save key in default location
• press again enter if you don’t want to add
a password to your key
2. Add key to your account
• copy public key (if you used the default
location: ~/.ssh/id_ed25519.pub)
xclip -sel clip < ~/.ssh/id_ed25519.pub
1
– mv day01.py Downloads: Moves day01.py
to the Downloads folder
– mv day01.py day02.py: Renames day01.py
to day02.py
• Copy a file cp:
– cp source dest: Copies the source file to the
destination.
– cp day01.py day02.py: Copies day01.py
and saves it as day02.py
– cp -r aoc aoc2: Copies the folder aoc and
saves it as aoc2. You need to add -r to recur-
sively copy all files in the folder.
• touch filename create a file with the filename.
– touch day01.py creates day01.py.
• ls: Lists all files and folder in the current folder
• ls folder: Lists all files and folders in folder
• mkdir name: Creates a folder with the name.
• if xclip is not installed, open file and copy
the key manually
• go to User Settings > SSH Keys to add
the ssh key to your gitlab account
3. Go to course repository: https://gitlab.com/lamdv
1/programming-with-python-2022
4. Fork repository (your fork must be public !) Fork
5. Open a terminal and change directory to your doc-
uments folder
6. Clone forked repository
git clone git@gitlab.com:<your account name>
/programming-with-python-2022.git
Overview Git

Important Commands Undo Changes

• configure git
git config --global user.name "your name"
git config --global user.email "your email"
• git add <filename> to add local changes to stag-
ing area
• git commit -m "commit message" to create new
‘save point’
• use git reset to reset repository to a previous commit
(all later commits will be deleted), e.g., git reset
c4edd723 where c4edd723 is the commit hash (use
git log to view git history)
• use git revert to reset repository to previous com-
mit, but keeping the log intact (add as new commit,
commits in between stay intact)
Advanced Information

• git push to add your commit to the remote repos- More information about git, like merging, branching etc.,
itory (pushed files are visible for us) can be found at https://git-scm.com/docs

• git status to get an overview about local changes

• if you work from multiple locations use git pull

to update your local files with the current status of
the remote repository (otherwise you might create
a merge conflict)

Miniconda
This description is intended for the pool computers. If
you use a different system, adjust the steps accordingly.
Download miniconda:
1. Go to https://docs.conda.io/en/latest/miniconda.
html
2. Download Miniconda3 Linux 64-bit
3. Open a Terminal.
4. Go to Downloads cd Downloads.
Install miniconda:
1. Make Miniconda executable by chmod +x
Miniconda3-latest-Linux-x86_64.sh
2. Install Miniconda
./Miniconda3-latest-Linux-x86_64.sh
3. Press enter to read the license agreement.
4. Type yes to accept.
5. Press enter to accept the default location in your
home folder.
6. Type yes to initialize conda.
7. Close the terminal and start a new one.
It should show you something like (base)
username@bioXX:~$.
You are in the base environment.
8. conda --version should result in conda 4.12.0.
Create an environment
• We want to create a new environment with Python
3.10.
• You create a new environment using coda create
-n $NAME [package_spec ...].
• Replace $NAME with the name for your environment,
e.g.: pyprog.
• Specify the Python version with python=3.10. This
installs the latest version of Python 3.10 which is
compatible with all other packages.
• conda create -n pyprog python=3.10 and ac-
cept the listed packages (y).
• To activate the new environment type conda
activate pyprog.
• The installed Python version (python --version)
should be Python 3.10.6.