Bioapps Container

This container is intended to collect most of the commonly used Bioinformatics software packages used on Rocket and Comet, and provide them in a single, easy to use format, without all of the complexity of many module load and module unload commands.

Jump straight to the Bioapps container software lists:

• Main software packages included
• Python modules
• R libraries

With almost limitless combinations of bioinformatics tools that can be used together it is very difficult to ensure that any given set of software modules which have been provisioned on Comet can be used alongside any other set of modules.

Multiple versions of Python, C compilers and runtimes, and dependencies mean that almost every single unique set of software which is intended to be used together needs to be validated and tested to make sure that no modules conflict - bwa may need version X of a runtime, but samtools could require version Y of the same runtime, and therefore it is impossible (or at least strongly inadvisable due to unpredictable behaviour in such a scenario) to use both tools in the same pipeline at once. As more and more modules are added, this becomes a combinatorial explosion of software and versions problem… which some of our users have already experienced.

By building all of the common bioinformatics tools in one container, with one C compiler, one version of Python, and one set of their dependencies we can guarantee that this set of software will work without conflicting with each other - and the unknown side affects of such version conflicts.

It also means we can use one set of tools on a local workstation or HPC without changing our workflow.

The Bioapps container is stored in the /nobackup/shared/containers directory and is accessible to all users of Comet. You do not need to take a copy of the container file; it should be left in its original location.

You can find the container files here:

• /nobackup/shared/containers/bioapps.2026.05.sif
• /nobackup/shared/containers/bioapps.2026.04.sif
• /nobackup/shared/containers/bioapps.2026.03.sif
• /nobackup/shared/containers/bioapps.2026.02.sif

We normally recommend using the latest (date) version of the container unless you have a specific need for an earlier version of software. Changes in software versions are listed in the table below.

We have provided a convenience script that will automate all of steps needed to run applications inside the container, and access your $HOME, /scratch and /nobackup directories to just two simple commands.

• /nobackup/shared/containers/bioapps.2026.05.sh

Just source this file and it will take care of loading apptainer, setting up your bind directories and calling the exec command for you - and give you a single command called container.run (instead of the really long apptainer exec command) to then run anything you want inside the container, for example - to run bowtie2:

$ source /nobackup/shared/containers/bioapps.2026.05.sh
$ container.run bowtie2 -U /nobackup/proj/my_project/fastq_data/file1.fq

You can continue to use the container.run command as many times as you need in the same script or same bash session:

$ source /nobackup/shared/containers/bioapps.2026.05.sh
$ container.run bowtie2 -U /nobackup/proj/my_project/fastq_data/file1.fq
$ container.run samtools
$ container.run bwameth
$ container.run hisat2 --version
$ container.run python3
$ container.run R
$ container.run convert3d
... etc

We strongly recommend that you use this helper script and the container.run command to run software from inside the container as it will always ensure that you have correctly set up the bind directories for you and you are using the correct container version.

As long as you use the container.run method to launch the applications, you will automatically be able to read and write to files in your $HOME, /scratch and /nobackup directories.

If you run any of the applications inside the container manually, without using the container.run helper you will need to use the –bind argument to apptainer to ensure that all relevant directories are exposed within the container.

Do remember that the container filesystem itself cannot be changed - so you won't be able to write or update to /usr/local, /opt, /etc or any other internal folders - keep output directories restricted to the three areas listed above.

The following databases / data files are already available on Comet and are automatically linked/configured to be used by the software in this container. They can also be used outside of the container by referencing the Location on Comet path.

You should not attempt to download duplicates of these data sets either into your $HOME area, or to your project areas under /nobackup. If an update to a data set is needed, please contact us.

All of the following software packages are available within the Bio apps container. Please check the Included From field to see which version of the container the software was introduced from.

Except where noted, all of the commands listed below are available in the $PATH and you do not need to supply their full directory name, i.e. the following is sufficient:

$ container.run bbmap.sh

You do not need to run:

$ container.run /opt/bbmap/bbmap.sh

Note: All binaries are compiled for the AMD Epyc CPU architecture of Comet with the CFLAGS=-O3 -march=znver5 -pipe flags with GCC 14, on top of any existing optimisation flags set by each application. All binaries are also stripped of debugging symbols with strip -g to reduce their on-disk and in-memory size requirements.

• (1) - bcl-convert is a vendor provided binary (proprietary to Illumina) and unlike all other listed software has not been recompiled for Comet.
• (2) - Tophat 1 & 2 are pre-compiled binaries from the developer - they do not build easily on modern compilers, and hence are not recompiled for Comet.

The Amrfinder data files are pre-installed and ready to use. At installation time Amrfinder was installed using DEFAULT_DB_DIR=/opt/amrfinder/db, so no command line parameters or environment variables are necessary in order to use the data files.

• /opt/amrfinder/db - Location of the Amrfinder data files inside the container
• /nobackup/shared/data/amrfinder - Location of the Amrfinder data files outside the container, on the Comet filesystem
• Current data size: 240 MB

No configuration is necessary to use the installed data files - they work as-is. e.g. assuming an input file named test_prot.fa in your project directory:

$ source /nobackup/shared/containers/bioapps.2026.06.sh
$ container.run amrfinder -p /nobackup/proj/comet_abc123/test_prot.fa
Running: amrfinder -p test_prot.fa
Software directory: /usr/local/bin/
Software version: 4.2.7
Reverting to hard coded directory: /opt/amrfinder/db/latest
Database directory: /opt/amrfinder/db/2026-05-15.1
Database version: 2026-05-15.1
AMRFinder protein-only search
  - include -n NUC_FASTA, --nucleotide NUC_FASTA and -g GFF_FILE, --gff GFF_FILE options to add translated searches
  - include -O ORGANISM, --organism ORGANISM option to add mutation searches and suppress common proteins
Running blastp
Running hmmsearch
Making report
...
...
...
amrfinder took 5 seconds to complete

• For more information on using amrfinderplus, see: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus#examples
• Test file: test_prot.fa.gz - download, gzip -d, and use as in the test example above
  • Downloaded from: https://github.com/ncbi/amr/blob/master/test_prot.fa

The Antismash data files are already pre-installed and ready to use by antismash within this container. Antismash integrates data files into it's Python module tree, so this has been completed for you already; no command line parameters or environment variables are required.

• /usr/local/lib/python3.12/dist-packages/antismash/databases - Location of the antismash database files inside the container
• /nobackup/shared/data/antismash - Location of the downloaded antismash database files outside the container, on the Comet filesystem
• Current database size: 9 GB

Do not try to download updates to the Antismash data files - this requires write access to the Antismash module folders. Instead if an update is needed contact us and we will arrange a new container image to be built with the latest Antismash and matching data files.

In addition, there are hashed versions of the database files inside the Antismash module tree inside the container:

• /usr/local/lib/python3.12/dist-packages/antismash/modules

You do not need to change any configuration to use the Antismash data files - it is ready to use and will load them automatically from their installed location, e.g, assuming you have an input file named GCF_000203835.1_ASM20383v1_genomic.gbff in your project directory:

$ source /nobackup/shared/containers/bioapps.2026.06.sh
$ container.run antismash /nobackup/proj/comet_abc123/GCF_000203835.1_ASM20383v1_genomic.gbff

Will, after a minute or two, produce an output directory named after the input file, in this case GCF_000203835.1_ASM20383v1_genomic/:

$ ls GCF_000203835.1_ASM20383v1_genomic/
css                                      NC_003888.3.region001.gbk  NC_003888.3.region008.gbk  NC_003888.3.region015.gbk  NC_003888.3.region022.gbk  NC_003888.3.region029.gbk
GCF_000203835.1_ASM20383v1_genomic.gbk   NC_003888.3.region002.gbk  NC_003888.3.region009.gbk  NC_003888.3.region016.gbk  NC_003888.3.region023.gbk  NC_003903.1.region001.gbk
GCF_000203835.1_ASM20383v1_genomic.json  NC_003888.3.region003.gbk  NC_003888.3.region010.gbk  NC_003888.3.region017.gbk  NC_003888.3.region024.gbk  NC_003903.1.region002.gbk
GCF_000203835.1_ASM20383v1_genomic.zip   NC_003888.3.region004.gbk  NC_003888.3.region011.gbk  NC_003888.3.region018.gbk  NC_003888.3.region025.gbk  regions.js
images                                   NC_003888.3.region005.gbk  NC_003888.3.region012.gbk  NC_003888.3.region019.gbk  NC_003888.3.region026.gbk
index.html                               NC_003888.3.region006.gbk  NC_003888.3.region013.gbk  NC_003888.3.region020.gbk  NC_003888.3.region027.gbk
js                                       NC_003888.3.region007.gbk  NC_003888.3.region014.gbk  NC_003888.3.region021.gbk  NC_003888.3.region028.gbk

When viewed in a browser, the HTML report in index.html should be somewhat similar to the image below:

• For more information on the use of Antismash: https://docs.antismash.secondarymetabolites.org/command_line/
• Test file: gcf_000203835.1_asm20383v1_genomic.gbff.gz - download, gzip -d, then use as the test example above
  • Downloaded from: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/203/835/GCF_000203835.1_ASM20383v1/

The Bakta databases have been downloaded and are ready to use within the container environment. The environment variable $BAKTA_DB is configured to point to the correct location of the database files, as listed below, so you do not need to set any command line arguments or make any additional changes to access them:

• /opt/bakta/db - Location of the Bakta databases inside the container
• /nobackup/shared/data/bakta - Location of the Bakta databases outside the container, on the Comet filesystem
• Current database size: 80 GB

Do not try to update the Bakta database files within the container. If you want to update Bakta and/or the databases, please contact us and we will create a new or replacement container with the updated version of Bakta and download the replacement database files for you.

An example of using Batka. Assuming you have the file sample_genome.fa in your project directory:

$ source /nobackup/shared/containers/bioapps.2026.06.sh
$ container.run bakta /nobackup/proj/comet_abs123/sample_genome.fa
Bakta v1.12.0

Parse genome sequences...
	imported: 17
	filtered & revised: 17
	contigs: 17

Start annotation...
predict tRNAs...
	found: 286
predict tmRNAs...
	found: 0
predict rRNAs...
	found: 11
predict ncRNAs...
	found: 1
predict ncRNA regions...
	found: 0
predict CRISPR arrays...
	found: 0
predict & annotate CDSs...
	predicted: 8068 
	discarded length: 0
	discarded spurious: 5
	revised translational exceptions: 0
	detected IPSs: 3
...

• For more information on the use of Bakta, see: https://github.com/oschwengers/bakta#examples
• Test genome file: sample_genome.fa.gz - download, gzip -d and use in the example as above
  • Downloaded from https://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/

The databases used by Eggnog have been downloaded already using download_eggnog_data.py after the Bioapps container was created. To use these databases you must pass the –data_dir parameter when calling the Eggnog tools.

• /opt/eggnog/db - Location of data files inside the container
• /nobackup/shared/data/eggnog - Location of data files outside the container on the Comet filesystem
• Current data size: 47 GB

You should not attempt to update these databases yourself. If you do wish to have a newer version of eggnog and the associated databases, please contact us and we will create or replace the Bioapps container with the new versions and update the databases in the shared data directory.

Example use of Eggnog-mapper. Assuming you have an input file named proteins.txt in your project directory:

$ source /nobackup/shared/containers/bioapps.2026.06.sh
$ container.run emapper.py --data_dir /opt/eggnog/db -i /nobackup/proj/comet_abc123/proteins.txt -o proteins_output
#  emapper-2.1.13
  /opt/bin/diamond blastp -d '/opt/eggnog/db/eggnog_proteins.dmnd' -q '/nobackup/proj/comet_abc123/proteins.txt' \
  --threads 1 -o '/nobackup/proj/comet_abc123/proteins_output.emapper.hits' \
  --tmpdir '/nobackup/proj/comet_abc123/emappertmp_dmdn_ju_fukx6' \
  --sensitive --iterate -e 0.001 --top 3  --outfmt 6 \
  qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp
  ...
  Functional annotation of hits...
3 16.677483081817627 0.18 q/s (% mem usage: 5.80, % mem avail: 94.23)
Done
Result files:
   /nobackup/proj/comet_abc123/proteins_output.emapper.hits
   /nobackup/proj/comet_abc123/proteins_output.emapper.seed_orthologs
   /nobackup/proj/comet_abc123/proteins_output.emapper.annotations

================================================================================

Total hits processed: 3
Total time: 2917 secs
FINISHED

• For more information on the use of Eggnog-mapper: https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.13
• Test file: proteins.txt.gz - download, gzip -d, and use per the example shown above

The various Meme databases have already been downloaded and are ready to use. At the point Meme was compiled and installed, the parameter –with-db=/opt/meme/db was used to set the location of the databases, as listed below, so no further command line arguments or changes are necessary in order to use them:

• /opt/meme/db - Location of the Meme databases inside the container
• /nobackup/shared/data/meme - Location of the Meme databases outside the container, on the Comet filesystem
• Current data size: 64 GB

Example Meme test. Assuming you have the file lex0.fna in your project directory:

$ source /nobackup/shared/containers/bioapps.2026.06.sh
$ container.run meme lex0.fna -oc meme_example_output -p 1 -dna -mod zoops -nmotifs 3 -revcomp
Writing results to output directory 'meme_example_output'.
BACKGROUND: using background model of order 0
PRIMARY (classic): n 16 p0 16 p1 0 p2 0
SEQUENCE GROUP USAGE-- Starts/EM: p0; Trim: p0; pvalue: p0; nsites: p0,p1,p2
SEEDS: maxwords 3067 highwater mark: seq 16 pos 192
BALANCE: samples 16 chars 3067 nodes 1 chars/node 3067
Initializing the motif probability tables for 2 to 16 sites...
nsites = 16
Done initializing.

seqs=    16, min_w= 136, max_w=  200, total_size=     3067

motif=1
SEED DEPTHS: 2 4 8 16
SEED WIDTHS: 8 11 15 21 29 41 50
em: w=  50, psites=  16, iter=  10 
motif=2
SEED DEPTHS: 2 4 8 16
SEED WIDTHS: 8 11 15 21 29 41 50
em: w=  50, psites=  16, iter=  10 
motif=3
SEED DEPTHS: 2 4 8 16
SEED WIDTHS: 8 11 15 21 29 41 50
em: w=  50, psites=  16, iter=   0
$

This should create a folder named meme_example_output with the following files:

$ ls meme_example_output/
logo1.eps  logo2.eps  logo3.eps  logo_rc1.eps  logo_rc2.eps  logo_rc3.eps  meme.html  meme.xml
logo1.png  logo2.png  logo3.png  logo_rc1.png  logo_rc2.png  logo_rc3.png  meme.txt

When the HTML file meme.html is viewed it should look like this:

• For more information on the use of Meme: https://meme-suite.org/meme/doc/overview.html?man_type=web
• Test file: lex0.fna.gz - download, gzip -d and run as per the example above
  • Downloaded from: https://gensoft.pasteur.fr/docs/meme/5.1.1/examples/example-datasets/?C=S;O=A

Unfortunately Miniphy is written to run from the installation directory itself, including input/, output/ and logs/ folders - this is not ideal in a multi-user environment.

To run Miniphy you must set several variables for each run:

• MINIPHY_INPUT - Your input file directory; if unset, this will default to $HOME/.bioapps_container/miniphy/input
• MINIPHY_OUTPUT - Output directory; if unset, this will default to $HOME/.bioapps_container/miniphy/output
• MINIPHY_INTER - Intermediate/temporary file directory; if unset, this will default to $HOME/.bioapps_container/miniphy/intermediate
• MINIPHY_LOGS - Logs produced during the run; if unset, this will default to $HOME/.bioapps_container/miniphy/logs

In most cases your input and output directories should probably be within a project directory - if left unset the above defaults will be used.

Also, the Miniphy software is configured by a single file named config.yaml inside the installation directory. So that multiple users do not overwrite each others files, we have created a specific runtime wrapper just for Miniphy. Instead of using container.run, please instead use container.run_miniphy; this will create a small (64MB) image in your home directory which will save changes you make to config.yaml (this is the same as for Phylign, below).

Our advice is to write small scripts to drive the output of Miniphy, for example:

#!/bin/bash

cd /opt/miniphy
./create_batches.py meta_file.tsv -d input

Then you can call container.run_miniphy to execute the script, the example below will map the Miniphy input/ and output/ directories to your project folder:

$ source /nobackup/shared/containers/bioapps.2026.06.sh
$ export MINIPHY_INPUT=/nobackup/proj/comet_abc123/my_input
$ export MINIPHY_OUTPUT=/nobackup/proj/comet_abc123/my_output
$ container.run_miniphy miniphy_script.sh

If you want to edit the values of config.yaml to change how Miniphy itself works (e.g. search parameters), you can do so by editing the file from inside the container environment:

$ source /nobackup/shared/containers/bioapps.2026.06.sh
$ container.run_miniphy vi /opt/miniphy/config.yml

• For more information on the use of Miniphy, see: https://github.com/karel-brinda/MiniPhy

All of the NCBI Blast databases are already pre-downloaded and ready to use via blastp and similar tools. The environment variable $BLASTDB is configured to point to the correct location of the database files, as listed below, so you do not need to add any command line arguments or make any further changes to access them:

• /opt/blast/db - NCBI database location inside the Bioapps container
• /nobackup/shared/data/blastplus - NCBI database location outside the container, on the Comet filesystem
• Current size: the complete NCBI Blast dataset on Comet is more than 3.8TB in size - do not attempt to download your own copy of this data!

Example of using NCBI Blast+. Assuming you have the input file uniprotkb_proteome_UP000009255_2026_06_19.fasta in your project directory, and to search the nr database:

$ source /nobackup/shared/containers/bioapps.2026.06.sh
$ container.run blastp -query uniprotkb_proteome_UP000009255_2026_06_19.fasta -db nr
BLASTP 2.17.0+

Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF
excluding environmental samples from WGS projects
           1,093,519,741 sequences; 414,572,423,463 total letters

• For more information about the Blast databases: https://ftp.ncbi.nlm.nih.gov/blast/documents/blastdb.html
• For more information about the use of NCBI Blast+: https://www.ncbi.nlm.nih.gov/books/NBK279690/
• Test file: uniprotkb_proteome_up000009255_2026_06_19.fasta.gz - download, gzip -d and use per example above
  • Downloaded from: https://www.uniprot.org/proteomes/UP000009255

Phylign already has all data files downloaded. Unfortunately Phylign is written to run from the installation directory itself, including input/, output/ and logs/ folders - this is not ideal in a multi-user environment.

Data files are in the following locations:

• /opt/phylign/db - Location of the database files inside the container
• /nobackup/shared/data/phylign - Location of the files outside the container on the Comet filesystem
• Current size: 92 GB

Please do not attempt to download additional or later versions of the Phylign databases. If you need updates then please contact us and we will arrange an update of the container and update the files on the Comet shared data area.

To run Phylign you must set several variables for each run:

• PHYLIGN_INPUT - Your input file directory; if unset, this will default to $HOME/.bioapps_container/phylign/input
• PHYLIGN_OUTPUT - Output directory; if unset, this will default to $HOME/.bioapps_container/phylign/output
• PHYLIGN_INTER - Intermediate/temporary file directory; if unset, this will default to $HOME/.bioapps_container/phylign/intermediate
• PHYLIGN_LOGS - Logs produced during the run; if unset, this will default to $HOME/.bioapps_container/phylign/logs

In most cases your input and output directories should probably be within a project directory - if left unset the above defaults will be used.

Also, the Phylign software is configured by a single file named config.yaml inside the installation directory. So that multiple users do not overwrite each others files, we have created a specific runtime wrapper just for Phylign. Instead of using container.run, please instead use container.run_phylign; this will create a small (64MB) image in your home directory which will save changes you make to config.yaml.

Our advice is to write small scripts to drive the output of Phylign, for example:

#!/bin/bash

cd /opt/phylign
make match
make map

Then you can call container.run_phylign to execute the script, in the example below this will map the Phylign input/ and output/ directories to your project folder:

$ source /nobackup/shared/containers/bioapps.2026.06.sh
$ export PHYLIGN_INPUT=/nobackup/proj/comet_abc123/my_input
$ export PHYLIGN_OUTPUT=/nobackup/proj/comet_abc123/my_output
$ container.run_phylign phylign_script.sh

If you want to edit the values of config.yaml to change how Phylign itself works (e.g. search parameters), you can do so by editing the file from inside the container environment:

$ source /nobackup/shared/containers/bioapps.2026.06.sh
$ container.run_phylign vi /opt/phylign/config.yml

• For more information on the use of Phylign, including several examples, see: https://github.com/karel-brinda/phylign

In addition to the standalone applications listed above, the following Python modules are installed (i.e. they are available if you use python3 installed from the container with a normal import module syntax in your code).

Normally you would be able to use these modules in your code if running Python as follows:

$ source /nobackup/shared/containers/bioapps.2026.03.sh
$ container.run python3 <myscript.py>

This list only includes modules which have been explicitly installed. The standard Python built-ins are still available: sqlite, json, etc.

In addition to the standalone applications listed above, the following R libraries are installed (i.e. they are available to use in the R and Rscript commands started from the container, and by using the normal library(module) syntax in your code).

Normally you would be able to use these modules in your code if running R as follows (obviously choose the correct version of the container runtime helper to suit your needs):

$ source /nobackup/shared/containers/bioapps.2026.05.sh
$ container.run Rscript <myscript.R>

This list only includes the R libaries which have been explicitly installed, or brought in as dependencies by other libraries. The standard R libraries are still available: base, splines, stats, utils, etc.

Build script:

• Note that the build script will automatically tag the container filename with YYYY.MM for a simple version naming scheme.
• To install bcl-convert the build script must be run from a directory which has a copy of bcl-convert-4.4.6-2.el8.x86_64.rpm - this is not free to download - if it is not found then the installation will skip it.

#!/bin/bash

IMAGE_DATE=`date +%Y.%m`

echo "Loading modules..."
module load apptainer

echo ""
echo "Building container..."
export APPTAINER_TMPDIR=/scratch

echo ""
echo "Container will have date suffix $IMAGE_DATE"


# You must supply a copy of bc-convert*.rpm in this
# folder below. If it is not present then the install
# of this tool will be skipped.
SOURCE_DIR=`pwd`

BCL_RPM="bcl-convert-4.4.6-2.el8.x86_64.rpm"

echo ""
echo "Checking source files..."
if [ -s "$SOURCE_DIR/$BCL_RPM" ]
then
	echo "- Found - $SOURCE_DIR/$BCL_RPM"
else
	echo "- WARNING - $SOURCE_DIR/$BCL_RPM is MISSING"
	echo ""
	echo "Press return to continue or Control+C to exit and fix"
	read	
fi


apptainer build --bind $SOURCE_DIR:/mnt bioapps.$IMAGE_DATE.sif bioapps.def 2>&1 | tee bioapps.log

Container definition:

Bootstrap: docker
From: ubuntu:noble

####################################################################
#
# Bio apps container
# ==================
# This is a runtime environment for a large set of bioinformatics tools.
# Please see: 
#	https://hpc.researchcomputing.ncl.ac.uk/dokuwiki/dokuwiki/doku.php?id=advanced:software:bioapps
#
# ======================================
#
# NAME : WORKING
#	LINK
#
# ======================================
# bamutil : Yes
#	https://github.com/statgen/bamUtil/
#
# bcftools :
#	https://github.com/samtools/bcftools
#
# bowtie2 : Yes
#	https://github.com/BenLangmead/bowtie2
#
# Bwa : Yes
#	https://github.com/lh3/bwa
#
# Bwa-mem2 : Yes
#	https://github.com/bwa-mem2/bwa-mem2/releases/tag/v2.3
#
# Bwa-meth : Yes
#	https://github.com/brentp/bwa-meth
#
# Samtools : Yes
#	https://github.com/samtools/samtools
#
# Sambamba : Yes
#	https://github.com/biod/sambamba
#
# Seqkit : Yes
#	https://github.com/shenwei356/seqkit
#
# methyldackel : Yes
#	https://github.com/dpryan79/MethylDackel
#
# minimap : Yes
#	https://github.com/lh3/minimap2
#
# bedtools2 : Yes
#	https://github.com/arq5x/bedtools2/archive/refs/heads/master.zip
#
# bam-readcount : Yes
#	https://github.com/genome/bam-readcount
#
# hisat2 : Yes
#	https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download
#
# StringTie : Yes
#	http://ccb.jhu.edu/software/stringtie/dl
#
# gffcompare : Yes
#	http://ccb.jhu.edu/software/stringtie/dl
#
# htseq-count : Yes
#	https://pypi.python.org/packages/source/H/HTSeq
#
# picard : Yes
#	https://github.com/broadinstitute/picard/releases/download
#
# seqan-library : Yes
#	https://github.com/seqan/seqan
#
# regtools : Yes
#	https://github.com/griffithlab/regtools
#
# RSeQC : Yes
#	https://rseqc.sourceforge.net/#download-rseqc
#
# Tophat : Yes
#	https://github.com/DaehwanKimLab/tophat
#	
####################################################################

%post
    # Prevent interactive prompts
    export DEBIAN_FRONTEND=noninteractive

####################################################################
#
# Basic system packages
#
####################################################################

    # Update & install only necessary packages
    apt-get update
	apt-get install -y \
		apt-utils \
		wget \
		autoconf \
		cmake \
		rpm2cpio \
		cpio \
		build-essential \
		man-db \
		tar \
		unzip \
		git \
		aptitude \
		golang-go \
		python3-pip \
		gcc-14 \
		g++-14 \
		gfortran-14 \
		openmpi-bin \
		openmpi-common \
		libopenmpi-dev \
		libgomp1 \
		autoconf \
		vim \
		libhts-dev \
		libncurses-dev \
		libbz2-dev \
		liblz4-dev \
		openjdk-25-jre \
		libbigwig-dev \
		libgsl-dev \
		libxml2-dev \
		libssl-dev \
		libpng-dev \
		liblapack-dev \
		libboost-dev \
		libboost-system-dev \
		libboost-thread-dev
	ln -s /usr/bin/python3 /usr/bin/python
	
    # Clean up APT cache to save space
    apt-get clean 

	# Any Python modules installed via pip go here
	# pip install NAME --break-system-packages
	
	# Remove any Python cache files after pip
	pip3 cache purge

#################################################################################
#
# This is all the custom stuff needed to build the various bioinformatics tools
#
#################################################################################

	# This flag needs to be set to indicate which CPU architecture we
	# are optimising for.
	AMD_ARCH=1

	if [ "$AMD_ARCH" = "1" ]
	then
		# Compiling on AMD Epyc
		export BASE_CFLAGS="-O3 -march=znver5 -pipe"
		export BASE_CFLAGS_ALT="-O3 -march=native -pipe"
		export MAKE_JOBS=8
	else
		# Compiling on generic system
		export BASE_CFLAGS="-O"
		export BASE_CFLAGS_ALT="-O"
		export MAKE_JOBS=8
	fi
	
	export CPPFLAGS=""
	export CFLAGS="$BASE_CFLAGS -I/opt/include"
	export CFLAGS_ALT="$BASE_CFLAGS_ALT -I/opt/include"
	export CXXFLAGS="$CFLAGS"
	export CC=gcc-14
	export CXX=g++-14
	export FC=gfortran-14
	export LD_LIBRARY_PATH=/opt/lib:$LD_LIBRARY_PATH
	export PATH=/opt/bin:$PATH

	###############################################################################
	# Tell R to use the newer version of GCC when it needs to compile.
	# R 'helpfully' ignores standard CC/CFLAG/etc environment variables and
	# uses its own mechanism for setting the C/C++ and optimisation flags to
	# use. Override those by writing /root/.R/Makevars instead.
	###############################################################################
	mkdir -p /root/.R/
	echo "CC=$CC" > /root/.R/Makevars
	echo "CXX=$CXX" >> /root/.R/Makevars
	echo "CFLAGS=$CFLAGS" >> /root/.R/Makevars
	echo "CXXFLAGS=$CFLAGS" >> /root/.R/Makevars
	echo "CMAKE_C_COMPILER=$CC" >> /root/.R/Makevars
	echo "CMAKE_CXX_COMPILER=$CXX" >> /root/.R/Makevars
	echo "F77=$FC" >> /root/.R/Makevars

	echo ""
	echo "Post-OS-install setup for Bio apps container"
	echo "============================================"

	# A download place for external libraries
	mkdir -p /src/zipped
	
	# Where installations go
	mkdir -p /opt/bin
	mkdir -p /opt/include
	mkdir -p /opt/lib
	mkdir -p /opt/man
	
	echo ""
	echo "Install Python2 - for Tophat1"
	echo "============================="
	cd /src
	wget -q https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tgz -O /src/zipped/python2.tgz
	cd /src
	tar -zxf /src/zipped/python2.tgz
	cd Python-2.7.18
	./configure \
		--prefix=/opt/python2 \
		--disable-ipv6 \
		--enable-shared=no \
		--enable-optimizations
	make clean
	make -j4 build_all
	make altinstall
	
	echo ""
	echo "Install Tophat 1"
	echo "==============="
	cd /src
	wget -q https://ccb.jhu.edu/software/tophat/downloads/tophat-1.4.1.Linux_x86_64.tar.gz -O /src/zipped/tophat-1.4.1.Linux_x86_64.tar.gz
	cd /opt
	tar -zxf /src/zipped/tophat-1.4.1.Linux_x86_64.tar.gz
	mv /opt/tophat-1.4.1.Linux_x86_64 /opt/tophat1
	
	# Amend the hash-bang line of the Python scripts to use the local version of Python 2
	cd /opt/tophat1
	file * | grep "Python script" | while read f
	do
		f_name=`echo $f | awk -F: '{print $1}'`
		sed -i 's|/usr/bin/env python|/opt/python2/bin/python2.7|g' "$f_name"
	done
	
	echo ""
	echo "Install Tophat 2"
	echo "================"
	cd /src
	wget -q https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz -O /src/zipped/tophat-2.1.1.Linux_x86_64.tar.gz
	cd /opt
	tar -zxf /src/zipped/tophat-2.1.1.Linux_x86_64.tar.gz
	mv /opt/tophat-2.1.1.Linux_x86_64 /opt/tophat2
	
	# Amend the hash-bang line of the Python scripts to use the local version of Python 2
	cd /opt/tophat2
	file * | grep "Python script" | while read f
	do
		f_name=`echo $f | awk -F: '{print $1}'`
		sed -i 's|/usr/bin/env python|/opt/python2/bin/python2.7|g' "$f_name"
	done
	
	echo ""
	echo "0a. Install latest R"
	echo "==================="
	apt-get install -y --no-install-recommends software-properties-common dirmngr
	wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
	add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
	apt-get install -y --no-install-recommends r-base

	echo ""
	echo "0b. Install R modules"
	echo "====================="

	# Install BioConductor
	Rscript -e 'install.packages("BiocManager", repos="https://cloud.r-project.org")'
	Rscript -e 'BiocManager::install(version = "3.22")'
	# Install DEXSeq
	Rscript -e 'BiocManager::install("DEXSeq")'	

	echo ""
	echo "1. Download / install bwa"
	echo "========================="
	cd /src/zipped
	wget -q https://github.com/lh3/bwa/archive/refs/tags/v0.7.19.tar.gz -O bwa-v0.7.19.tar.gz
	cd /src
	tar -zxf zipped/bwa-v0.7.19.tar.gz
	cd bwa-0.7.19/
	cp Makefile Makefile.old
	
	# Strip out hardcoded CC and CFLAGS to use our own
	cat Makefile.old | grep -v "^CC=" | grep -v "^CFLAGS=" > Makefile
	
	make -j$MAKE_JOBS
	strip -g bwa
	cp -v bwa /opt/bin
	cp -v qualfa2fq.pl /opt/bin
	cp -v xa2multi.pl /opt/bin
	cp -v bwa.1 /opt/man
	
	echo ""
	echo "2. Download / install bwa-mem2"
	echo "=============================="
	cd /src/zipped
	wget -q https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.3/Source_code_including_submodules.tar.gz -O bwa-mem2-v2.3.tar.gz
	cd /src
	tar -zxf zipped/bwa-mem2-v2.3.tar.gz
	cd bwa-mem2-2.3
	
	# bwa-mem2 Patch 1
	cp ext/safestringlib/safeclib/abort_handler_s.c ext/safestringlib/safeclib/abort_handler_s.c.old
	cat ext/safestringlib/safeclib/abort_handler_s.c.old | \
		sed 's/#include "safeclib_private.h"/#include <stdlib.h>\n#include "safeclib_private.h"/g' > ext/safestringlib/safeclib/abort_handler_s.c
		
	# bwa-mem2 Patch 2
	cp ext/safestringlib/safeclib/strcasecmp_s.c ext/safestringlib/safeclib/strcasecmp_s.c.old
	cat ext/safestringlib/safeclib/strcasecmp_s.c.old | \
		sed 's/#include "safeclib_private.h"/#include <ctype.h>\n#include "safeclib_private.h"/g' > ext/safestringlib/safeclib/strcasecmp_s.c
	
	# bwa-mem2 Patch 3
	cp ext/safestringlib/safeclib/strcasestr_s.c ext/safestringlib/safeclib/strcasestr_s.c.old
	cat ext/safestringlib/safeclib/strcasestr_s.c.old | \
		sed 's/#include "safeclib_private.h"/#include <ctype.h>\n#include "safeclib_private.h"/g' > ext/safestringlib/safeclib/strcasestr_s.c
	
	make -j$MAKE_JOBS
	strip -g bwa-mem2*
	cp -v bwa-mem2* /opt/bin
		
	echo ""
	echo "3a. Download / install bwa-meth - toolshed"
	echo "=========================================="
	cd /src/zipped
	wget -q https://pypi.python.org/packages/source/t/toolshed/toolshed-0.4.0.tar.gz -O toolshed-0.4.0.tar.gz
	cd /src
	tar -zxf zipped/toolshed-0.4.0.tar.gz
	cd toolshed-0.4.0
	python setup.py install
	
	echo ""
	echo "3b. Download / install bwa-meth"
	echo "=========================================="
	cd /src/zipped
	wget -q https://github.com/brentp/bwa-meth/archive/master.zip -O bwa-meth.zip
	cd /src
	unzip zipped/bwa-meth.zip
	cd bwa-meth-master
	cp -v bwameth.py /opt/bin
	ln -sv /opt/bin/bwameth.py /opt/bin/bwameth
	
	echo ""
	echo "4. Download / install samtools"
	echo "=============================="
	cd /src/zipped
	wget -q https://github.com/samtools/samtools/releases/download/1.23/samtools-1.23.tar.bz2 -O samtools-1.23.tar.bz2
	cd /src
	tar -jxf zipped/samtools-1.23.tar.bz2
	cd samtools-1.23
	./configure --prefix=/opt
	make -j$MAKE_JOBS
	make install
	strip -g /opt/bin/samtools
	
	echo ""
	echo "5a. Download / install sambamba - ldc"
	echo "====================================="
	cd /src/zipped
	wget -q https://github.com/ldc-developers/ldc/releases/download/v1.42.0-beta3/ldc2-1.42.0-beta3-linux-x86_64.tar.xz -O ldc2-1.42.0-beta3-linux-x86_64.tar.xz
	cd /src
	tar -xf zipped/ldc2-1.42.0-beta3-linux-x86_64.tar.xz
	
	# Temporarily add ldc2 to the path
	PATH=/src/ldc2-1.42.0-beta3-linux-x86_64/bin:$PATH
	LIBRARY_PATH=/src/ldc2-1.42.0-beta3-linux-x86_64/lib
	
	echo ""
	echo "5b. Download / install sambamba"
	echo "==============================="
	cd /src/zipped
	wget -q https://github.com/biod/sambamba/archive/refs/heads/master.zip -O sambamba-master.zip
	cd /src
	unzip zipped/sambamba-master.zip
	cd sambamba-master
	CC=gcc-14 make release
	strip -g bin/sambamba-1.0.1
	cp -v bin/sambamba-1.0.1 /opt/bin/sambamba
	
	echo ""
	echo "6. Download / install seqkit"
	echo "============================"
	cd /src/zipped
	wget -q https://github.com/shenwei356/seqkit/archive/refs/tags/v2.12.0.tar.gz -O seqkit-v2.12.0.tar.gz
	cd /src
	tar -zxf zipped/seqkit-v2.12.0.tar.gz
	cd seqkit-2.12.0/seqkit
	go build
	strip -g seqkit
	cp -v seqkit /opt/bin
	
	echo ""
	echo "6. Download / install methyldackel"
	echo "=================================="
	cd /src/zipped
	wget -q https://github.com/dpryan79/MethylDackel/archive/refs/tags/0.6.1.tar.gz -O methyldackel-0.6.1.tar.gz
	cd /src
	tar -zxf zipped/methyldackel-0.6.1.tar.gz
	cd MethylDackel-0.6.1/
	make -j$MAKE_JOBS LIBBIGWIG=/lib/x86_64-linux-gnu/libBigWig.a
	strip -g MethylDackel
	cp -v MethylDackel /opt/bin
	ln -s /opt/bin/MethylDackel /opt/bin/methyldackel
	
	echo ""
	echo "7. Download / install minimap"
	echo "=================================="
	cd /src/zipped
	wget -q https://github.com/lh3/minimap2/archive/refs/tags/v2.30.tar.gz -O minimap2-v2.30.tar.gz
	cd /src
	tar -zxf zipped/minimap2-v2.30.tar.gz
	cd minimap2-2.30
	cp Makefile Makefile.old
	# Strip out hardcoded CFLAGS to use our own
	cat Makefile.old | grep -v "^CFLAGS=" > Makefile
	make -j$MAKE_JOBS
	strip -g minimap2
	cp -v minimap2 /opt/bin
	
	echo ""
	echo "8. Download / install bedtools2"
	echo "==============================="
	cd /src/zipped
	wget -q https://github.com/arq5x/bedtools2/archive/refs/heads/master.zip -O bedtools2-master.zip
	cd /src
	unzip zipped/bedtools2-master.zip
	cd bedtools2-master
	cp Makefile Makefile.old
	# Strip out hardcoded compiler name to use our own
	cat Makefile.old | sed 's/= g++/= g++-14/g' > Makefile
	make -j$MAKE_JOBS
	strip -g bin/bedtools
	cp -v bin/* /opt/bin
	
	echo ""
	echo "9. Install bam-readcount"
	echo "========================"
	cd /src/zipped
	wget -q https://github.com/genome/bam-readcount/archive/refs/heads/master.zip -O bam-readcount-master.zip
	cd /src
	unzip zipped/bam-readcount-master.zip
	cd bam-readcount-master
	mkdir build
	cd build
	cmake ..
	# This does not like parallel builds - it ends up out of sequence...
	make
	strip -g bin/bam-readcount
	cp -v bin/bam-readcount /opt/bin
	
	echo ""
	echo "10. Install hisat2"
	echo "=================="
	cd /src/zipped
	wget -q https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download -O hisat2-2.2.1.zip
	cd /src
	unzip zipped/hisat2-2.2.1.zip
	cd hisat2-2.2.1
	cp Makefile Makefile.old
	# Strip out hardcoded compiler name to use our own
	cat Makefile.old | \
		sed 's/CC = /CC = gcc-14 #/g' | \
		sed 's/CPP = /CPP = g++-14 #/g' | \
		sed 's/RELEASE_FLAGS  =/RELEASE_FLAGS  = $(CFLAGS) /g' > Makefile
	make -j$MAKE_JOBS
	strip -g hisat2-align-l
	strip -g hisat2-align-s
	strip -g hisat2-build-l
	strip -g hisat2-align-s
	strip -g hisat2-inspect-l
	strip -g hisat2-inspect-s
	strip -g hisat2-repeat
	cp -v hisat2 hisat2-align* hisat2-inspect* hisat2-repeat hisat2_*.py extract_*.py /opt/bin
	
	echo ""
	echo "11. Install stringtie"
	echo "======================"
	cd /src/zipped
	wget -q https://ccb.jhu.edu/software/stringtie/dl/stringtie-3.0.3.tar.gz -O stringtie-3.0.3.tar.gz
	cd /src
	tar -zxf zipped/stringtie-3.0.3.tar.gz
	cd stringtie-3.0.3/
	make -j$MAKE_JOBS release
	strip -g stringtie
	cp -v stringtie /opt/bin
	cp -v prepDE.py3 /opt/bin/prepDE.py
	
	echo ""
	echo "12. Install gffcompare"
	echo "======================"
	cd /src/zipped
	wget -q https://ccb.jhu.edu/software/stringtie/dl/gffcompare-0.12.9.tar.gz -O gffcompare-0.12.9.tar.gz
	cd /src
	tar -zxf zipped/gffcompare-0.12.9.tar.gz
	cd gffcompare-0.12.9
	make -j$MAKE_JOBS
	strip -g gffcompare
	strip -g trmap
	cp -v gffcompare /opt/bin
	cp -v trmap /opt/bin
	
	echo ""
	echo "13. Install htseq"
	echo "================="
	pip3 install HTSeq --break-system-packages
	
	echo ""
	echo "14. Install picard"
	echo "=================="
	cd /src/zipped
	wget -q https://github.com/broadinstitute/picard/releases/download/3.4.0/picard.jar -O picard-3.4.0.jar
	cd /src
	cp -v zipped/picard-3.4.0.jar /opt/bin/picard.jar
	# We also set up a "java -jar picard.jar" helper alias
	# via an entry in the post-install %environment section
	
	echo ""
	echo "15a. Install flexbar - seqan"
	echo "============================"
	#cd /src/zipped
	#wget -q https://github.com/seqan/seqan/archive/refs/tags/seqan-v2.5.2.tar.gz -O seqan-v2.5.2.tar.gz 
	#cd /src
	#tar -zxf zipped/seqan-v2.5.2.tar.gz
	#cd seqan-seqan-v2.5.2
	#mkdir build
	#cd build
	#cmake ..
	#make -j$MAKE_JOBS
	#cd ../build/bin/ 
	#/bin/ls | grep -v ^demo | grep -v ^test | while read B
	#do
	#	strip -g $B
	#	cp -v $B /opt/bin
	#done
	
	#echo ""
	#echo "15b. Install flexbar - Intel threading blocks"
	#echo "============================================="
	#cd /src/zipped
	#wget -q https://github.com/uxlfoundation/oneTBB/archive/refs/tags/4.4.6.tar.gz -O tbb-4.4.6.tar.gz
	#cd /src
	#tar -zxf zipped/tbb-4.4.6.tar.gz
	#cd oneTBB-4.4.6
	
	# Patch for GCC13+
	# Found here: https://github.com/bambulab/BambuStudio/pull/1882/changes/d3459cb1b9f791531fe24b0558c581117243eade
	#cp include/tbb/task.h include/tbb/task.h.old
	#cat include/tbb/task.h.old | \
	#	sed 's/task\* next_offloaded\;/tbb\:\:task\* next_offloaded\;/g' > include/tbb/task.h
		
	# Mangle CXXFLAGS to allow compiling the old code against new GCC
	#CXXFLAGS="-O3 -march=znver4 -pipe -std=c++14" make
	
	#cp -v build/linux_intel64_gcc_cc13_libc2.39_kernel6.8.0_release/*.so /opt/lib
	#cp -v build/linux_intel64_gcc_cc13_libc2.39_kernel6.8.0_release/*.so.2 /opt/lib
	#cp -v -a include/tbb /opt/include
	
	# Reset CXXFLAGS back again
	#export CXXFLAGS="$CFLAGS"
	
	#echo ""
	#echo "15c. Install flexbar"
	#echo "===================="
	#cd /src/zipped
	#wget -q https://github.com/seqan/flexbar/archive/refs/tags/v3.5.0.tar.gz -O flexbar-v3.5.0.tar.gz
	#cd /src
	#tar -zxf zipped/flexbar-v3.5.0.tar.gz 
	#cd flexbar-3.5.0
	# Copy in the seqan 'library' - which is C++ code in header files...
	#cp -a /src/seqan-seqan-v2.5.2/include .
	#cmake .
	#make -j$MAKE_JOBS
	
	echo ""
	echo "16. Install regtools"
	echo "===================="
	cd /src/zipped
	wget -q https://github.com/griffithlab/regtools/archive/refs/tags/1.0.0.tar.gz -O regtools-1.0.0.tar.gz
	cd /src
	tar -zxf zipped/regtools-1.0.0.tar.gz
	cd regtools-1.0.0
	mkdir build
	cd build
	cmake ..
	make -j$MAKE_JOBS
	strip -g regtools
	cp -v regtools /opt/bin
	
	echo ""
	echo "17. Install rseqc"
	echo "================="
	cd /src/zipped
	wget -q https://sourceforge.net/projects/rseqc/files/RSeQC-5.0.1.tar.gz/download -O RSeQC-5.0.1.tar.gz
	cd /src
	# This tar file was created with AD/Domain user owner/group info
	# ignore it when extracting...
	tar --no-same-owner -zxf zipped/RSeQC-5.0.1.tar.gz
	cd RSeQC-5.0.1/
	python setup.py install
	
	echo ""
	echo "18. Install bcftools"
	echo "====================="
	cd /src/zipped
	wget -q https://github.com/samtools/bcftools/releases/download/1.23/bcftools-1.23.tar.bz2 -O bcftools-1.23.tar.bz2
	cd /src
	tar -jxf zipped/bcftools-1.23.tar.bz2
	cd bcftools-1.23
	./configure --prefix=/opt --enable-libgsl
	make
	make install
	
	echo ""
	echo "19. Install bamutil"
	echo "==================="
	cd /src/zipped
	wget -q https://github.com/statgen/bamUtil/archive/refs/tags/v1.0.15.tar.gz -O bamutil-1.0.15.tar.gz
	cd /src
	tar -zxf zipped/bamutil-1.0.15.tar.gz
	cd bamUtil-1.0.15
	
	# Public git://github.com calls no longer work in 2026+
	# Patch it out to https instead.
	cp Makefile.inc Makefile.inc.old
	cat Makefile.inc.old | sed 's/git clone git/git clone https/g' > Makefile.inc
	
	CFLAGS="$BASE_CFLAGS_ALT -I/opt/include"
	make cloneLib
	make
	make install INSTALLDIR=/opt/bin
	strip -g /opt/bin/bam
	CFLAGS="$BASE_CFLAGS -I/opt/include"
	
	echo ""
	echo "20. Install bowtie2"
	echo "==================="
	cd /src/zipped
	wget -q https://github.com/BenLangmead/bowtie2/archive/refs/tags/v2.5.5.tar.gz -O bowtie2-2.5.5.tar.gz
	cd /src
	tar -zxf zipped/bowtie2-2.5.5.tar.gz
	cd bowtie2-2.5.5
	mkdir build
	cd build
	cmake ..
	make -j$MAKE_JOBS
	strip -g bowtie2-*
	cp -v bowtie2-* /opt/bin
	cd ..
	cp -v bowtie2 /opt/bin
	cp -v bowtie2-inspect /opt/bin
	cp -v bowtie2-build /opt/bin
	
	echo ""
	echo "21. Install bcl_convert"
	echo "======================="
	cd /src
	if [ -s /mnt/bcl-convert-4.4.6-2.el8.x86_64.rpm ]
	then
		mkdir bcl-convert
		cd bcl-convert
		rpm2cpio /mnt/bcl-convert-4.4.6-2.el8.x86_64.rpm | cpio -idmv
		cp usr/bin/bcl-convert /opt/bin
	else
		echo "WARNING!!!! - Unable to find bcl_convert.rpm - this will be skipped"
	fi
	
	# Remove all src packages
	echo ""
	echo "Cleaning up downloaded src tree"
	echo "=================================="
	cd
	rm -rf /src
	pip3 cache purge
	
	echo ""
	echo "7. All done"

%environment
	export PATH=/opt/bin:$PATH
	export LD_LIBRARY_PATH=/opt/lib:$LD_LIBRARY_PATH
	export CFLAGS="-O -I/opt/include"
	export CXXFLAGS="$CFLAGS"
	export CC=gcc-14
	export CXX=g++-14
	export FC=gfortran-14
	export OMPI_CC=gcc-14
	export MANPATH=/opt/man
	alias picard="java -jar /opt/bin/picard.jar"

%runscript

Run file

You should source this file in order to use the container.run command. This should have the current container image name set as the IMAGE_NAME parameter:

#!/bin/bash

module load apptainer

IMAGE_NAME=/nobackup/shared/containers/bioapps.2026.02.sif

container.run() {
	# Run a command inside the container...
	# automatically bind the /scratch and /nobackup dirs
	# pass through any additional parameters given on the command line
	apptainer exec --bind /scratch:/scratch --bind /nobackup:/nobackup ${IMAGE_NAME} $@
}

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