From 2cfb1440f3c23f74add84aef043d40d3d7437a5d Mon Sep 17 00:00:00 2001
From: Fanny Wegner <fwegner@imm.uzh.ch>
Date: Fri, 15 Mar 2024 13:26:38 +0100
Subject: [PATCH] Update 2 files
- /exercises/UNIX_HPC_cheat_sheet.md
- /exercises/UNIX_HPC_exercise_instructions.md
---
exercises/UNIX_HPC_cheat_sheet.md | 11 +++++++++--
exercises/UNIX_HPC_exercise_instructions.md | 4 ++--
2 files changed, 11 insertions(+), 4 deletions(-)
diff --git a/exercises/UNIX_HPC_cheat_sheet.md b/exercises/UNIX_HPC_cheat_sheet.md
index 1cf526f..14450c3 100644
--- a/exercises/UNIX_HPC_cheat_sheet.md
+++ b/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:
diff --git a/exercises/UNIX_HPC_exercise_instructions.md b/exercises/UNIX_HPC_exercise_instructions.md
index e95ce5c..bac8c4f 100644
--- a/exercises/UNIX_HPC_exercise_instructions.md
+++ b/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
```
--
GitLab