Changes between Version 1 and Version 2 of cypress/SingularityDockerhub

Timestamp:

03/02/23 14:04:52 (14 months ago)

Author:

fuji

Comment:

—

cypress/SingularityDockerhub

@@ -18 +18 @@
 singularity pull docker://ubuntu:14.04
 }}}
+
+=== Example : [https://github.com/moshi4/FastDTLmapper FastDTLmapper] ===
+This tool requires many python packages and needs those to set up both python2 and python3. Fortunately, the developer provides Docker Images so we can use a Docker image and generate a Sigularity image.
+
+On Centos7 computing node, (need 'idev'),
+{{{
+module load singularity/3.9.0
+singularity pull docker://ghcr.io/moshi4/fastdtlmapper:latest
+}}}
+This command creates ‘fastdtlmapper_latest.sif’, which is the Singularity Image. You can rename/transfer it as you like.
+
+To run it to show ‘help’,
+{{{
+singularity exec fastdtlmapper_latest.sif FastDTLmapper -h
+}}}
+
+To run it with the minimum test dataset,
+Assuming the example dataset is extracted under /lustre/project/group/user/fastdtlmapper, where 'group' is the group name and 'user' is the user name,
+{{{
+export SINGULARITYENV_TMPDIR=/tmp
+export SINGULARITY_BINDPATH=/lustre/project/group/user:/home/user,$TMPDIR:/tmp
+singularity exec fastdtlmapper_latest.sif FastDTLmapper -i fastdtlmapper/example/minimum_dataset/fasta/ -t fastdtlmapper/example/minimum_dataset/species_tree.nwk -o fastdtlmapper/output_minimum
+}}}
+
+For Slurm batch jobs,
+{{{
+#!/bin/bash
+#SBATCH --job-name=fastDLmapper # Job Name
+#SBATCH --partition=centos7    # Partition
+#SBATCH --qos=normal           # 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
+}}}
+