diff --git a/exercises/UNIX_HPC_exercise_instructions.md b/exercises/UNIX_HPC_exercise_instructions.md index 3f5f2339708c08909c063ffe03b5f9e237297163..bc577e6710a2f212427e70c9b61b6896f8bff578 100644 --- a/exercises/UNIX_HPC_exercise_instructions.md +++ b/exercises/UNIX_HPC_exercise_instructions.md @@ -292,14 +292,9 @@ 2. **On the command line, loop through all fasta files starting with "ompA" using `var1`** and print the name to standard output. * Once you type `for` and press `ENTER`, the shell will recognise the syntax and you can continue writing the for-loop line by line. It will evaluate the whole command only after you entered `done`. -3. **In your editor, write a simple script called `copy_and_rename.sh`.** - - **Preparation:** It's easiest if you write your script locally and then transfer it via SFTP of your command line client (Termius/Notepad++) to the cluster into your `intro_to_unix` directory. - - **For BBEdit users:** You can turn on syntax highlighting either by saving the file as a .sh file or by selecting "Unix Shell Script" in the drop-down menu at the very bottom (it says "Text file" by default). - - **For Notepad++ users:** You can turn on syntax highlighting by selecting "shell" in the "Language" menu. +3. **In VSCode, write a simple script called `copy_and_rename.sh`.** + * Create an empty text file and save it into your `intro_to_unix` directory as `copy_and_rename.sh`. * In a for loop, go through all fasta files starting with "ompA". * Copy each fasta file. For the name of the new copy, replace "ompA" with "outerMembraneProteinA". * Run the script from within your `intro_to_unix` folder. @@ -439,8 +434,10 @@ **Objective:** running software from singularity images and submitting jobs to Science Cluster >**BEFORE WE START** -Please run the following command: +Please run the following commands: ```sh +mkdir /home/$USER/scratch/singularity_tmpdir +echo "export SINGULARITY_TMPDIR=/home/$USER/scratch/singularity_tmpdir" >> $HOME/.bashrc echo "export SINGULARITY_BINDPATH=/scratch,/data,/home/$USER,/shares/amr.imm.uzh" >> $HOME/.bashrc source $HOME/.bashrc ```