Commit c5c50cbd authored by root's avatar root

July 2020 update

parent 0026b2b1
This diff is collapsed.
#!/bin/bash
#SBATCH --ntasks=1
#SBATCH --time=0:05:00
#SBATCH --GRES=abaqus+5
module purge
source /usr/local/module/spartan_old.sh
module load ABAQUS/6.14.2-linux-x86_64
# Run the job 'Door'
abaqus job=Door
#!/bin/bash
#SBATCH --partition=physical
#SBATCH --time=1:00:00
module purge
source /usr/local/module/spartan_old.sh
module load ABINIT/8.0.8b-intel-2016.u3
abinit < tbase1_x.files >& log
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=2015ABRicate-test.slurm
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
source /usr/local/module/spartan_old.sh
module load ABRicate/0.8.7-spartan_intel-2017.u2
# The command to actually run the job
abricate ecoli_rel606.fasta
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=ABRicate-test.slurm
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
module load spartan_2019
module load foss/2019b
module load abricate/0.9.9-perl-5.30.0
# The command to actually run the job
abricate ecoli_rel606.fasta
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=ABySS-test.slurm
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
module load ABySS/2.0.2-goolf-2015a
# Assemble a small synthetic data set
tar xzvf test-data.tar.gz
sleep 20
abyss-pe k=25 name=test in='test-data/reads1.fastq test-data/reads2.fastq'
# Calculate assembly contiguity statistics
abyss-fac test-unitigs.fa
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=ABySS-test.slurm
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
module load spartan_2019
module load foss/2019b
module load abyss/2.1.5
# Assemble a small synthetic data set
tar xzvf test-data.tar.gz
sleep 20
abyss-pe k=25 name=test in='test-data/reads1.fastq test-data/reads2.fastq'
# Calculate assembly contiguity statistics
abyss-fac test-unitigs.fa
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=2015ADMIXTURE-test.slurm
# Run with two threads
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module load ADMIXTURE/1.3.0
# Untar sample files, run application
# See admixture --help for options.
tar xvf hapmap3-files.tar.gz
admixture -j2 hapmap3.bed 1
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=2019ADMIXTURE-test.slurm
# Run with two threads
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
module load spartan_2019
module load admixture/1.3.0
# Untar sample files, run application
# See admixture --help for options.
tar xvf hapmap3-files.tar.gz
admixture -j2 hapmap3.bed 1
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=2015AFNI-test.slurm
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
source /usr/local/module/spartan_old.sh
module load AFNI/linux_openmp_64-spartan_intel-2017.u2-20190219
# Untar dataset and run script
tar xvf ARzs_data.tgz
./@ARzs_analyze
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=AFNI-test.slurm
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
module load spartan_2019
module load foss/2019b
module load afni/18.3.00-python-3.7.4
# Untar dataset and run script
tar xvf ARzs_data.tgz
./@ARzs_analyze
This is incomplete; still getting the tgz files organised. LL20200707
#!/bin/bash
#SBATCH --job-name="2015ANSYStest"
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < OscillatingPlate.inp > OscillatingPlate.db
#!/bin/bash
# Job name and partition
#SBATCH --job-name=ARAGORN-test.slurm
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
source /usr/local/module/spartan_old.sh
module load ARAGORN/1.2.36-GCC-4.9.2
# Run the application
aragorn -o results sample.fa
#!/bin/bash
# Add your project account details here.
# SBATCH --account=XXXX
#SBATCH --partition=gpgpu
#SBATCH --ntasks=4
#SBATCH --time=1:00:00
module purge
source /usr/local/module/spartan_old.sh
module load Amber/16-gompi-2017b-CUDA-mpi
srun /usr/local/easybuild/software/Amber/16-gompi-2017b-CUDA-mpi/amber16/bin/pmemd.cuda_DPFP.MPI -O -i mdin -o mdout -inf mdinfo -x mdcrd -r restrt
Array job indices can be specified in various number of ways.
A job array with index values between 0 and 31:
#SBATCH --array=0-31
A job array with index values of 1, 2, 5, 19, 27:
#SBATCH --array=1,2,5,19,27
A job array with index values between 1 and 7 with a step size of 2 (i.e. 1, 3, 5, 7):
#SBATCH --array=1-7:2
As with all Slurm directives, the SBATCH command can be applied within the batch script or on the command line.
To convert a directory of files to include an array ID see the following example:
$ touch aaa.fastq.gz bbb.fastq.gz ccc.fastq.gz ddd.fastq.gz
$ ls
aaa.fastq.gz bbb.fastq.gz ccc.fastq.gz ddd.fastq.gz
$ n=1; for f in *fastq.gz; do mv "$f" "$((n++))$f"; done
$ ls
1aaa.fastq.gz 2bbb.fastq.gz 3ccc.fastq.gz 4ddd.fastq.gz
See also the Octave array example in /usr/local/common/Octave.
#!/bin/bash
#SBATCH --job-name="file-array"
#SBATCH --ntasks=1
#SBATCH --time=0-00:15:00
#SBATCH --array=1-5
# Note: SLURM defaults to running jobs in the directory
# where they are submitted, no need for $PBS_O_WORKDIR
mkdir ${SLURM_ARRAY_TASK_ID}
#!/bin/bash
# Job name and partition
#SBATCH --job-name=2015BAMM-test.slurm
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Speciation-extinction analyses
# You must have an ultrametric phylogenetic tree.
# Load the environment variables
module purge
source /usr/local/module/spartan_old.sh
module load BAMM/2.5.0-spartan_intel-2017.u2
# Example from: `http://bamm-project.org/quickstart.html`
# To run bamm you must specify a control file.
# The following is for diversification.
# You may wish to use traits instead
# bamm -c template_trait.txt
bamm -c template_diversification.txt
#!/bin/bash
# Job name and partition
#SBATCH --job-name=BAMM-test.slurm
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Speciation-extinction analyses
# You must have an ultrametric phylogenetic tree.
# Load the environment variables
module purge
module load spartan_2019
module load foss/2019b
module load bamm/2.5.0
# Example from: `http://bamm-project.org/quickstart.html`
# To run bamm you must specify a control file.
# The following is for diversification.
# You may wish to use traits instead
# bamm -c template_trait.txt
bamm -c template_diversification.txt
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=2015BBMap-test.slurm
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
source /usr/local/module/spartan_old.sh
module load BBMap/36.62-intel-2016.u3-Java-1.8.0_71
# See examples at:
# http://seqanswers.com/forums/showthread.php?t=58221
reformat.sh in=sample1.fq out=processed.fq
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=BBMap-test.slurm
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
module load spartan_2019
module load bbmap/38.76
# See examples at:
# http://seqanswers.com/forums/showthread.php?t=58221
reformat.sh in=sample1.fq out=processed.fq
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=BEDTools-test.slurm
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
source /usr/local/module/spartan_old.sh
module load BEDTools/2.28.0-spartan_intel-2017.u2
# BEDTools has an extensive test suite; but the tests assumes the wrong
# location for the application!
# So all these tests need to be be modified to include:
# BT=$(which bedtools)
cp -r /usr/local/easybuild/software/BEDTools/2.27.1-intel-2017.u2/test/* .
find ./ -type f -exec sed -i -e 's/${BT-..\/..\/bin\/bedtools}/$(which bedtools)/g' {} \;
sh test.sh
# Specific example commands available here:
# https://bedtools.readthedocs.io/en/latest/content/example-usage.html#bedtools-intersect
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=BEDTools-test.slurm
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
module load spartan_2019
module load foss/2019b
module load bedtools/2.27.1
# BEDTools has an extensive test suite; but the tests assumes the wrong
# location for the application!
# So all these tests need to be be modified to include:
# BT=$(which bedtools)
cp -r /usr/local/easybuild/software/BEDTools/2.27.1-intel-2017.u2/test/* .
find ./ -type f -exec sed -i -e 's/${BT-..\/..\/bin\/bedtools}/$(which bedtools)/g' {} \;
sh test.sh
# Specific example commands available here:
# https://bedtools.readthedocs.io/en/latest/content/example-usage.html#bedtools-intersect
#!/bin/bash
# Set the number of processors that will be used.
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
# Set the walltime (5 hrs)
#SBATCH --time=5:00:00
# Load the environment variables
module purge
source /usr/local/module/spartan_old.sh
module load BLAST/2.2.26-Linux_x86_64
# Run the job
blastall -i ./rat-ests/rn_est -d ./dbs/rat.1.rna.fna -p blastn -e 0.05 -v 5 -b 5 -T F -m 9 -o rat_blast_tab.txt -a 8
#!/bin/bash
# Set the number of processors that will be used.
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
# Set the walltime (5 hrs)
#SBATCH --time=5:00:00
# Load the environment variables
module purge
module load spartan_2019
module load blast/2.10.0-linux_x86_64
# Run the job
blastall -i ./rat-ests/rn_est -d ./dbs/rat.1.rna.fna -p blastn -e 0.05 -v 5 -b 5 -T F -m 9 -o rat_blast_tab.txt -a 8
#!/bin/bash
#SBATCH --time=2:00:00
# Set up enviroment PATH
module purge
source /usr/local/module/spartan_old.sh
module load BWA/0.7.17-intel-2017.u2
module load SAMtools/1.9-intel-2017.u2
module load web_proxy
# Get source files
mkdir -p data/ref_genome
curl -L -o data/ref_genome/ecoli_rel606.fasta.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/017/985/GCA_000017985.1_ASM1798v1/GCA_000017985.1_ASM1798v1_genomic.fna.gz
sleep 30
gunzip data/ref_genome/ecoli_rel606.fasta.gz
curl -L -o sub.tar.gz https://downloader.figshare.com/files/14418248
sleep 60
tar xvf sub.tar.gz
mv sub/ data/trimmed_fastq_small
mkdir -p results/sam results/bam results/bcf results/vcf
# Run commands
bwa index data/ref_genome/ecoli_rel606.fasta
bwa mem data/ref_genome/ecoli_rel606.fasta data/trimmed_fastq_small/SRR2584866_1.trim.sub.fastq data/trimmed_fastq_small/SRR2584866_2.trim.sub.fastq > results/sam/SRR2584866.aligned.sam
samtools view -S -b results/sam/SRR2584866.aligned.sam > results/bam/SRR2584866.aligned.bam
samtools sort -o results/bam/SRR2584866.aligned.sorted.bam results/bam/SRR2584866.aligned.bam
#!/bin/bash
#SBATCH --time=2:00:00
# Set up enviroment PATH
module purge
module load spartan_2019
module load foss/2019b
module load bwa/0.7.17
module load samtools/1.9
module load web_proxy
# Get source files
mkdir -p data/ref_genome
curl -L -o data/ref_genome/ecoli_rel606.fasta.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/017/985/GCA_000017985.1_ASM1798v1/GCA_000017985.1_ASM1798v1_genomic.fna.gz
sleep 30
gunzip data/ref_genome/ecoli_rel606.fasta.gz
curl -L -o sub.tar.gz https://downloader.figshare.com/files/14418248
sleep 60
tar xvf sub.tar.gz
mv sub/ data/trimmed_fastq_small
mkdir -p results/sam results/bam results/bcf results/vcf
# Run commands
bwa index data/ref_genome/ecoli_rel606.fasta
bwa mem data/ref_genome/ecoli_rel606.fasta data/trimmed_fastq_small/SRR2584866_1.trim.sub.fastq data/trimmed_fastq_small/SRR2584866_2.trim.sub.fastq > results/sam/SRR2584866.aligned.sam
samtools view -S -b results/sam/SRR2584866.aligned.sam > results/bam/SRR2584866.aligned.bam
samtools sort -o results/bam/SRR2584866.aligned.sorted.bam results/bam/SRR2584866.aligned.bam
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=BEAST-test.slurm
# Run on 4 cores
#SBATCH --ntasks=4
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
source /usr/local/module/spartan_old.sh
module load Beast/2.3.1-intel-2016.u3
beast testRNA.xml
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=BEAST-test.slurm
# Run on 4 cores
#SBATCH --ntasks=4
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
module load spartan_2019
module load foss/2019b
module load beast/2.5.1
beast testRNA.xml
This diff is collapsed.
#!/bin/bash
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
# You might need an external license file
# export LM_LICENSE_FILE=port@licenseserver
module purge
source /usr/local/module/spartan_new.sh
module load COMSOL/5.2
# Example batch command from csiro.org.au
comsol batch -inputfile mymodel.mph -outputfile mymodelresult.mph -batchlog mybatch.log -j b1 -np 8 -mpmode owner
#!/bin/bash
# Name and Partition
#SBATCH --job-name=CPMD-test.slurm
# Run on two cores
#SBATCH --ntasks=2
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
source /usr/local/module/spartan_old.sh
module load CPMD/4.3-intel-2018.u4
# Example taken from Axek Kohlmeyer's classic tutorial
# http://www.theochem.ruhr-uni-bochum.de/~legacy.akohlmey/cpmd-tutor/index.html
srun -n 2 cpmd.x 1-h2-wave.inp > 1-h2-wave.out
#!/bin/bash
# Name and Partition
#SBATCH --job-name=CPMD-test.slurm
# Run on four cores
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL