update scripts and minor edits

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

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

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

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