Changes between Version 11 and Version 12 of cypress/SingularityDockerhub

Timestamp:

08/21/25 11:53:02 (3 months ago)

Author:

cbaribault

Comment:

Added workshop job script

cypress/SingularityDockerhub

@@ -109 +109 @@
 
 For Slurm batch jobs,
+
+'''For Workshop'''
+
+{{{
+#!/bin/bash
+#SBATCH --job-name=fastDLmapper # Job Name
+#SBATCH --partition=workshop7  # Partition
+#SBATCH --qos=workshop         # Quality of Service
+#SBATCH --time=0-24:00:00      # Wall clock time limit in Days-HH:MM:SS
+#SBATCH --nodes=1              # Node count required for the job
+#SBATCH --ntasks-per-node=1    # Number of tasks to be launched per Node
+#SBATCH --cpus-per-task=20     # Number of threads per task (OMP threads)
+#SBATCH --output=try_fastDLmapper.out       ### File in which to store job output
+#SBATCH --error=try_fastDLmapper.err        ### File in which to store job error messages
+ 
+# Load Singularity module
+module load singularity/3.9.0
+ 
+# Set $TMPDIR in containar to /tmp, keeping $TMPDIR in host (/local/tmp/...)
+export SINGULARITYENV_TMPDIR=/tmp
+ 
+# Mount the lustre directory to home, $TMPDIR to /tmp
+export SINGULARITY_BINDPATH=/lustre/project/group/user:/home/user,$TMPDIR:/tmp
+ 
+# Run container
+singularity exec fastdtlmapper_latest.sif FastDTLmapper -i fastdtlmapper/example/minimum_dataset/fasta/ -t fastdtlmapper/example/minimum_dataset/species_tree.nwk -o fastdtlmapper/output_minimum
+}}}
+
+
+'''Non Workshop'''
+
 {{{
 #!/bin/bash