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| general:computerenvironment:tasksetbash [2025/04/07 09:21] – freya | general:computerenvironment:tasksetbash [2026/01/13 10:33] (current) – felix | ||
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| + | <WRAP tabs> | ||
| + | * [[beh_molevol: | ||
| + | * [[beh_molevol: | ||
| + | * [[mbw_bioinf: | ||
| + | * [[mbw_bioinf: | ||
| + | * [[pbioc_basics: | ||
| + | * [[pbioc_basics: | ||
| + | * [[physaliacg: | ||
| + | </ | ||
| + | |||
| + | |||
| ====== Working with the command line ====== | ====== Working with the command line ====== | ||
| Line 81: | Line 92: | ||
| We have compiled a set of tasks for you that will deepen your knowledge about working with the BASH shell and will introduce some principles and dataformats which are common to bioinformatics. | We have compiled a set of tasks for you that will deepen your knowledge about working with the BASH shell and will introduce some principles and dataformats which are common to bioinformatics. | ||
| - | These exercises will come in the format of [[https:// | + | These exercises will come in the format of [[https:// |
| - | < | + | |
| - | Go ahead and download our exercises from GitHub via this [[https://github.com/BIONF/digital_competence|LINK]]. The easiest way to start the download is to click on the green "Code button" | + | - Now you can create |
| + | < | ||
| + | - Activate your new environment:< | ||
| + | < | ||
| + | === 2.2 Exercises === | ||
| + | |||
| + | - To start, [[https:// | ||
| + | <hidden Hint>The easiest way to start the download is to click on the green "Code button" | ||
| <figure git> | <figure git> | ||
| - | {{ :studentarea:felix:git.png?700 |}} | + | {{:general:computerenvironment:download_digital_competence.png?700|}} |
| < | < | ||
| **Starting download of the ZIP file.** | **Starting download of the ZIP file.** | ||
| </ | </ | ||
| </ | </ | ||
| - | + | </ | |
| - | === 2.2 Exercises === | + | - Unpack the directory with a [[https:// |
| - | [[general: | + | |
| - | < | + | - Now, make sure that the your '' |
| - | + | < | |
| - | This will open a window in your browser with which you can navigate to the `.ipynb` files of each exercise. The notebooks contain a set of instructions and some tasks. They also contain code cells in which you should document the command which solve the task. | + | |
| - | + | ||
| - | You can also use the code cells to experiment and find your solution, but we encourage you to try out all commands | + | |
| ==== 3. Using a computer cluster ==== | ==== 3. Using a computer cluster ==== | ||
| - | |||
| In the previous exercises you have learned to write commands and pipelines in the BASH shell. Now we want to look at how we can expand our analyses to large-scale analyses or datasets. For such resource heavy jobs we have a computer cluster available which is managed by the SLURM architecture. Please read through the [[https:// | In the previous exercises you have learned to write commands and pipelines in the BASH shell. Now we want to look at how we can expand our analyses to large-scale analyses or datasets. For such resource heavy jobs we have a computer cluster available which is managed by the SLURM architecture. Please read through the [[https:// | ||
| Line 111: | Line 126: | ||
| * Create a SLURM script file that executes the same command and run it on the cluster | * Create a SLURM script file that executes the same command and run it on the cluster | ||
| * Discuss with the other people in the course when best to use the computer cluster | * Discuss with the other people in the course when best to use the computer cluster | ||
| + | |||
| ==== 4. Environments ==== | ==== 4. Environments ==== | ||
| - | |||
| === .bashrc === | === .bashrc === | ||
| Line 125: | Line 140: | ||
| === Alias === | === Alias === | ||
| - | |||
| If you often use the same long command you can simplify your life by adding an alias to the end of .bashrc. | If you often use the same long command you can simplify your life by adding an alias to the end of .bashrc. | ||
| Line 155: | Line 169: | ||
| ---- | ---- | ||
| - | |||
| === $PATH === | === $PATH === | ||
| Line 228: | Line 241: | ||
| <WRAP tabs> | <WRAP tabs> | ||
| - | * [[ecoevo_molevol:course_introduction|EcoEvo main]] | + | * [[beh_molevol:start|EcoEvo main]] |
| - | * [[ecoevo_molevol: | + | * [[beh_molevol: |
| - | * [[mbw_bioinf: | + | * [[mbw_bioinf: |
| * [[mbw_bioinf: | * [[mbw_bioinf: | ||
| * [[pbioc_basics: | * [[pbioc_basics: | ||
| * [[pbioc_basics: | * [[pbioc_basics: | ||
| - | * [[:physaliacg: | + | * [[physaliacg: |
| </ | </ | ||