diff --git a/exercises/UNIX_HPC_cheat_sheet.md b/exercises/UNIX_HPC_cheat_sheet.md index 1cf526fa5b852849fb9f3952fceb3e765a812706..14450c3747cd44bc00d015307c0ddcb35efa207b 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 e95ce5c23f5e94191c0c6a26b8e9183ffd2ca510..bac8c4f58419a8dfb412112e437abf6ff19ffd16 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 ```