Software

BEAST2 

spack load beast2
beast

bedtools2 

spack load bedtools2
bedtools ...

bioperl 

spack load perl-bioperl
perl -e "use BioPerl; ...."

BLAST+

spack load blast-plus
blast...

Bohra

Bohra is a microbial genomics pipeline.

Bohra is made available on the cluster as a shared Apptainer container image.

You can use the apptainer/bohra module which will add convenient aliases to the bohra binary, which will run within the container.

See the Bohra wiki for usage information.

module load apptainer/bohra
# The following is required to use aliases in a non-interactive/SLURM batch script:
shopt -s expand_aliases
bohra test
bohra run ......

Bowtie2 

spack load bowtie2
bowtie2...

This assumes all input and output files are located in your home directory, which gets automatically made available in the container by Apptainer. Other paths will have to be explicitely mapped, in which case we need to use the apptainer run command excplictely pointing to the location of the container image. e.g. to map the /scratch/foo/data directory on /data in the container:

apptainer run --bind /tmp/test $APPTAINER_IMAGES/circlator_1.5.5.sif circlator test /tmp/test/outdir

Clustalw 

spack load clustalw
clustalw2 ...

Conda 

You can install miniconda under your user according to the instructions on the conda site (either with the bootstrap script or pip), or alternatively initialise your shell using the preinstalled Spack-provided miniconda:

spack load miniconda3
conda init bash
printf "if [ -s ~/.bashrc ]; then\n\tsource ~/.bashrc;\nfi\n" >> ~/.bash_profile

Then re-open a shell as instructed. This should initialise conda, making it available from that point on without the need for a spack load.

It is recommended to install related conda packages for a particular project within their own dedicated conda environment.

Diamond 

spack load diamond
diamond ...

Entrez Direct 

spack load entrezdirect
esearch ...

FastTree 

spack load fasttree
FastTree ...

FastQC 

spack load fastqc
fastqc

Flye 

spack load py-flye
flye ...

Gubbins

Genealogies Unbiased By recomBinations In Nucleotide Sequences - Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.

Gubbins is made available on the cluster as a shared Apptainer container image.

You can use the apptainer/gubbins module which will add convenient aliases to Gubbins scripts, such as run_gubbins.py, which will run within the container.

To use any of the aliases in a non-interactive/SLURM batch script, add the following in your script before using the alias: shopt -s expand_aliases.

See the Gubbins manual for usage information. Example:

module load apptainer/gubbins
# The following is required to use aliases in a non-interactive/SLURM batch script:
shopt -s expand_aliases
run_gubbins.py <FASTA alignment>

Guppy 

spack load ont-guppy
guppy_...

HMMER 

spack load hmmer
hmmsearch ...

Jupyter 

spack load py-jupyter
<load any other spack py- packages or modules etc you want to have available in your notebook>
jupyter-notebook

Take note of the URL displayed when starting jupyter-notebook. The Jupyter notebook web server will only be accessible locally on the server; You will need to access the URL in the browser running on the server (i.e. via an X2Go session; This would be the easiest option for most users), with X11 forwarding, or set up SSH port forwarding to access it from your local client browser.

On the X2Go XFCE desktop, open the Browser and access the Jupyter notebook URL (http://localhost:xxxx?token=…..).

This should work out of the box when you’re using Linux on the client side. On macOS and Windows, you would need to install an X-server.

connect via SSH, with the -Y option

 ssh koch.uod.otago.ac.nz -Y

start a browser with the Jupyter notebook URL. e.g.:

firefox http://localhost:8888?token=.........

e.g. if URL displayed is http://localhost:8888, forward to your local client with:

 ssh -vgL 8888:localhost:8888 koch.uod.otago.ac.nz

Then access the notebook URL http://localhost:8888?token=...... using your local browser.

When using Conda environments, Jupyter will not use the environment it is launched in. In order to make use of the packages installed in the environment, you will need to add a kernel (ipykernel) to your conda environment, either by installing the whole Jupyter package:

conda activate ....
...
conda install jupyter
jupyter-notebook

or alternatively:

conda activate .....
spack load py-jupyter
conda install ipykernel
ipython kernel install --user
jupyter-notebook

Then when creating a new Python notebook in Jupyter, make sure to select the Conda environment from the kernel dropdown.

Kraken2 

spack load kraken2
kraken2 ...

Reference databases can be found under /scratch/DATABASES.

Medaka 

spack load py-medaka
medaka_...

MetaPhlAn 

spack load py-metaphlan
metaphlan ...

muscle 

spack load muscle
muscle ...

Miniconda 

See Conda

minimap2 

spack load minimap2
minimap2 ...

Nanopolish 

Nanopolish is made available as an Apptainer container.

You can direcly run ‘nanopolish’ from the container with:

nanopolish-0.14.0.sif nanopolish ....

Alternatively you can enter an interactive shell in the container with:

nanopolish-0.14.0.sif /bin/bash

Nanopolish and its dependencies are located in /nanopolish.

This assumes all input and output files are located in your home directory, which gets automatically made available in the container by Apptainer. Other paths will have to be explicitely mapped, in which case we need to use the apptainer run command excplictely pointing to the location of the container image. e.g. to map the /tmp/foodir directory in the container:

apptainer run --bind /tmp/foodir $APPTAINER_IMAGES/nanopolish-0.14.0.sif nanopolish index -d /tmp/foodir reads.fasta

Nullarbor 

Nullarbor is made available as an Apptainer container.

Files in your $HOME directory as well as /scratch are automatically made available in the container by Apptainer.

To enter the container, run:

nullarbor-2.0.20191013.sif

All the nullarbor pipeline tools and dependencies should now be available. When finished, run exit to leave the container.

The default location of the reference databases are defined by these environment varables: KRAKEN_DEFAULT_DB, KRAKEN2_DEFAULT_DB, CENTRIFUGE_DEFAULT_DB

PhyloPhlAn 

spack load py-phylophlan
phylophlan ....

Prokka 

spack load prokka
prokka ....

Python 

By default the system Python will be used; python -V.

spack find python will show you additional installed versions that can be loaded with Spack:

spack load python@<version>
python -V

While you can install pip or conda packages in your local home directory as usual, several optimised python packages may already be installed and available for use via Spack.

spack find ^python@<version> | grep py- will show the list of Spack-installed pip packages available for the given Python version. These can be loaded in a similar way to make them available in python. e.g.

spack load py-numpy ^python@3.9

QIIME 2 

QIIME is made available as an Apptainer container.

Files in your $HOME directory as well as /scratch are automatically made available in the container by Apptainer.

qiime2-2022.8.sif qiime --version

R 

spack load r
R

While you should be able to download additional CRAN packages from within R, several common packages are already installed and available to be loaded with Spack before starting R. See spack find | grep r- to get a list of the installed R packages. These additional packages can be spack-loaded at the same time. e.g.:

spack load r r-units r-sp
R

RAxML 

spack load raxml
raxmlHPC ....

spack load raxml-ng
raxml-ng-mpi ....

RFPlasmid 

spack load rfplasmid
rfplasmid.py ....

RStudio 

RStudio is made available as an Apptainer container.

From a terminal in an X-enabled session (e.g. with FastX or X2Go), run the wrapper script rstudio_server_apptainer.sh. A remote browser window should then launch where you can sign in using your username and the generated password that is displayed in the terminal.

Any modules or Spack packages loaded before launching the script, should be available in your R session.

SAMtools 

spack load samtools
samtools ....

Kraken reference databases for QC can be found under /scratch/DATABASES.

SPAdes 

spack load spades
spades.py ....

SRA Tools 

spack load sra-tools
sra-....

TBProfiler 

TBProfiler is made available as an Apptainer container.

To run, prepend :code:’tb-profiler’ with the container image name:

tbprofiler-6.2.1.sif tb-profiler --version

Trinity 

Trinity is made available as an Apptainer container.

trinityrnaseq-2.15.0.sif
Trinity ....

Trycycler 

Trycycler is made available as an Apptainer container.

trycycler-0.5.0.sif
Trycycler ....

Unicycler 

Unicycler is made available as an Apptainer container.

unicycler-0.5.0.sif
unicycler ....

USEARCH 

See VSEARCH

VSEARCH 

spack load vsearch
vsearch ....