Updated course so is ready for next session

Author: StevenWingett

exercises.md

@@ -159,7 +159,7 @@ The links should be generated outside the file_list folder, in separate folders
 3. To what groups do you belong (the name of the required Linux command is quite intuitive)?  To what groups does the person who is running the course belong?  If you can't work out how to do this, then look in the `man` pages.
 
 ### b. 
-1. Write a single-line Bash command that takes the contents of the file letters.txt, sorts them alphabetically and then writes them to a new file named `sorted.txt`.
+1. Write a single-line Bash command that takes the contents of the file `letters.txt`, sorts them alphabetically and then writes them to a new file named `sorted.txt`.
 
 ### c. 
 1. Write a Bash command to download the file: https://raw.githubusercontent.com/StevenWingett/Bioinformatics_Computer_Cluster_Course/refs/heads/main/README.md

presentation.md

@@ -585,11 +585,11 @@ table {
 
 * Keeps the nodes all in contact with one another etc.
 
-* LMB cluster uses Slurm (updated recently)
+* LMB cluster uses **Slurm**
 
 ---
 
-## Using Slurm (2)
+## Slurm (2)
 
 * Slurm is open-source software for large and small Linux clusters
 
@@ -705,7 +705,7 @@ Slurm scripts:
 
     #!/bin/bash
     #SBATCH --job-name=test_job
-    #SBATCH --cpus-per-task=c
+    #SBATCH --cpus-per-task=1
     #SBATCH --mem=2G
     #SBATCH --mail-type=ALL
     #SBATCH --mail-user=$USER@mrc-lmb.cam.ac.uk
@@ -760,7 +760,7 @@ Run as:
 
 ---
 
-## Where to put data (Cluster)
+## Where to put data - Cluster
 
 * `~` (home directory) -  config files and scripts
 
@@ -770,11 +770,21 @@ Run as:
 
 * `/istore` or `/isilon` - a place to store data
 
-**Refer to Scientific Computing for further information**
+
+
+---
+
+## Where to put data - Cluster (2)
+
+* Your group may have its own dedicated storage area
+
+* Check your quota in the dashboard
+
+* **Refer to Scientific Computing for further information**
 
 ---
 
-## Where to put data (Cell Biology Xeon)
+## Where to put data - Cell Biology Xeon
 
 * `~` (home directory) -  config files and scripts
 

tutor_notes/answers.md

@@ -76,10 +76,12 @@ Version
 
 1.    
 `srun --pty bash`
+
 `exit`
 
 2.
 `srun -c 4 --mem=5G --pty bash`
+
 `exit` 
 
 #### d
@@ -111,15 +113,17 @@ Version
 
 #### *f
 
+`python3 make_fasta_files.py`
+
 Create script `array_job.slurm`, containing:
 
-      #!/bin/bash
-      #SBATCH --job-name=arrayjob_calc_gc
-      #SBATCH --ntasks=1
-      #SBATCH --cpus-per-task=1
-      #SBATCH --array=1-10
-
-      SAMPLE_ID=$((SLURM_ARRAY_TASK_ID))
-      echo $SAMPLE_ID
-      python3 calc_gc.py sample.$SAMPLE_ID.fa.gz
+    #!/bin/bash
+    #SBATCH --job-name=arrayjob_calc_gc
+    #SBATCH --ntasks=1
+    #SBATCH --cpus-per-task=1
+    #SBATCH --array=1-10
+
+    SAMPLE_ID=$((SLURM_ARRAY_TASK_ID))
+    echo $SAMPLE_ID
+    python3 calc_gc.py sample.$SAMPLE_ID.fa.gz