Update 2 files

- /exercises/UNIX_HPC_cheat_sheet.md
- /exercises/UNIX_HPC_exercise_instructions.md

exercises/UNIX_HPC_cheat_sheet.md

@@ -99,7 +99,14 @@ fi
 
 
 ## Running Singularity containers
-Running a container called `my_software_container` that contains a command called `my_software` (on a computation node)
+1) From sandbox: Running a container called `my_software_container` that has been sandboxed into `my_sandbox` and contains a command called `my_software` (on a computation node)
+`my_software` (on a computation node)
+```bash
+srun singularity exec my_sandbox my_software [parameters]             
+```
+
+
+2) From image: Running a container called `my_software_container` that contains a command called `my_software` (on a computation node)
 ```bash
 srun my_software_container.sif my_software [parameters]             
 ```
@@ -140,7 +147,7 @@ module load singularityce
 command1
 command2
 
-srun my_software_container.sif my_software [parameters]   
+srun singularity exec my_sandbox my_software [parameters]   
 ```
 
 Submit script as job to the computing nodes:

exercises/UNIX_HPC_exercise_instructions.md

@@ -454,7 +454,7 @@ source $HOME/.bashrc
       * 30 min runtime 
       * Give the job a sensible name to identify it
    * Load the `singularityce` module
-   * The software for generating the MSA is called `mafft`. It is installed via its singularity image which can be found here: `/shares/amr.imm.uzh/bioinfo/singularity/mafft_7.505--hec16e2b_0.sif`. 
+   * The software for generating the MSA is called `mafft`. It is installed via its singularity image which can be found here: `/shares/amr.imm.uzh/bioinfo/singularity/sandbox/mafft_7.505`. 
 
       `mafft` is a very convenient software which can recognise if you want to align DNA or proteins automatically. 
    * The command for `mafft` is as follows: 
@@ -483,7 +483,7 @@ source $HOME/.bashrc
    # load the Singularity module
    module load singularityce
    
-   /shares/amr.imm.uzh/bioinfo/singularity/mafft_7.505--hec16e2b_0.sif mafft all_ompA.fasta > all_ompA_msa.fasta
+   srun singularity exec /shares/amr.imm.uzh/bioinfo/singularity/sandbox/mafft_7.505 mafft all_ompA.fasta > all_ompA_msa.fasta
    ```