From f377ee0b4ca60caa4ca14f5519a25685cd435769 Mon Sep 17 00:00:00 2001
From: Fanny Wegner <fwegner@imm.uzh.ch>
Date: Fri, 15 Mar 2024 14:39:43 +0100
Subject: [PATCH] Update file UNIX_HPC_exercise_instructions.md
---
exercises/UNIX_HPC_exercise_instructions.md | 13 +++++--------
1 file changed, 5 insertions(+), 8 deletions(-)
diff --git a/exercises/UNIX_HPC_exercise_instructions.md b/exercises/UNIX_HPC_exercise_instructions.md
index 3f5f233..bc577e6 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
```
--
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