diff --git a/course_files/slurm/drosophila_genome_indexing.sh b/course_files/slurm/drosophila_genome_indexing.sh index 2fb58fe..5649bfc 100644 --- a/course_files/slurm/drosophila_genome_indexing.sh +++ b/course_files/slurm/drosophila_genome_indexing.sh @@ -9,7 +9,7 @@ # these lines are needed to source the mamba activate command # include them if you want to activate environments in your script eval "$(conda shell.bash hook)" -source $(mamba info --base)/etc/profile.d/mamba.sh +source $CONDA_PREFIX/etc/profile.d/mamba.sh # activate conda environment FIXME diff --git a/course_files/slurm/parallel_drosophila_mapping.sh b/course_files/slurm/parallel_drosophila_mapping.sh index d51ae8e..369a676 100644 --- a/course_files/slurm/parallel_drosophila_mapping.sh +++ b/course_files/slurm/parallel_drosophila_mapping.sh @@ -10,7 +10,7 @@ # these lines are needed to source the mamba activate command # include them if you want to activate environments in your script eval "$(conda shell.bash hook)" -source $(mamba info --base)/etc/profile.d/mamba.sh +source $CONDA_PREFIX/etc/profile.d/mamba.sh # activate conda environment mamba activate mapping diff --git a/course_files/slurm/parallel_turing_pattern.sh b/course_files/slurm/parallel_turing_pattern.sh index ea5cbd0..8d918bf 100644 --- a/course_files/slurm/parallel_turing_pattern.sh +++ b/course_files/slurm/parallel_turing_pattern.sh @@ -12,7 +12,7 @@ echo "Starting array: $SLURM_ARRAY_TASK_ID" # these lines are needed to source the mamba activate command # include them if you want to activate environments in your script eval "$(conda shell.bash hook)" -source $(mamba info --base)/etc/profile.d/mamba.sh +source $CONDA_PREFIX/etc/profile.d/mamba.sh # activate conda environment mamba activate scipy diff --git a/course_files/slurm/seqkit_singularity.sh b/course_files/slurm/seqkit_singularity.sh new file mode 100644 index 0000000..998ae8d --- /dev/null +++ b/course_files/slurm/seqkit_singularity.sh @@ -0,0 +1,10 @@ +#!/bin/bash +#SBATCH -p training # name of the partition to run job on +#SBATCH -D /home/FIX-YOUR-USERNAME/scratch/hpc_workshop/ # working directory +#SBATCH -o logs/seqkit.log # standard output file +#SBATCH -c 1 # number of CPUs. Default: 1 +#SBATCH --mem=1G # RAM memory. Default: 1G +#SBATCH -t 00:10:00 # time for the job HH:MM:SS. Default: 1 min + +# Your singularity command here +singularity FIXME \ No newline at end of file