====== 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:
* [[#individual_software_help|Main software packages included]]
* [[#python_modules|Python modules]]
* [[#r_libraries|R libraries]]
----
===== Why A Container? =====
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.
----
===== Running on Comet =====
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.2026.03.sif''
* ''/nobackup/shared/containers/bioapps.2026.02.sif''
We //normally// recommend using the latest (date) version of the container.
**Container Image Versions**
We //may// reference a specific container file, such as **bioapps.2026.03.sif**, but you should always check whether this is the most recent version of the container available. Simply ''ls'' the ''/nobackup/shared/containers'' directory and you will be able to see if there are any newer versions listed.
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.2026.03.sh''
There is a corresponding ''.sh'' script for //each version// of the container image we make available.
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 our ''bowtie2'' command as before:
$ source /nobackup/shared/containers/bioapps.2026.03.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.2026.03.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
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.
----
===== Individual Software Help =====
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.
^ Title ^ Included from ^ Files ^ Source Link ^ Description ^
| bamutil | 2026.02+ | ''bam'' | https://github.com/statgen/bamUtil/ | |
| bcftools | 2026.02+ | ''bcftools'' | https://github.com/samtools/bcftools | The plugins (e.g. //counts.so//, //contrast.so//, //prune.so//, etc) for ''bcftool'' are installed under ''/opt/libexec/bcftools'' and will be used automatically. |
| bcl_convert (1) | 2026.02+ | ''bcl-convert'' | https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert/downloads.html | Note that the use of ''bcl-convert'' is subject to the following licensing restrictions:\\ \\ - The software can only be used //"... for the purpose of processing and analyzing data generated from an Illumina genetic sequencing instrument owned and operated solely by (the University)"//\\ \\ - The software is only to be used for research purposes\\ \\ - The software can only be used with data generated from the Illumina instrument, and not any data generated from other sources |
| bowtie2 | 2026.02+ | ''bowtie2''\\ ''bowtie2-align-l''\\ ''bowtie2-align-s''\\ ''bowtie2-build-l''\\ ''bowtie2-build-s''\\ ''bowtie2-inspect-l''\\ ''bowtie2-inspect-s'' | https://github.com/BenLangmead/bowtie2 | |
| bwa | 2026.02+ | ''bwa''\\ ''qualfa2fq.pl''\\ ''xa2multi.pl'' | https://github.com/lh3/bwa | |
| bwa-mem2 | 2026.02+ | ''bwa-mem2''\\ ''bwa-mem2.avx''\\ ''bwa-mem2.avx2''\\ ''bwa-mem2.avx512bw''\\ ''bwa-mem2.sse41''\\ ''bwa-mem2.sse42'' | https://github.com/bwa-mem2/bwa-mem2 | Calling ''bwa-mem2'' will automatically select the most optimal version (e.g. ''avx'', ''avx2'' etc). |
| bwa-meth | 2026.02+ | ''bwameth.py''\\ ''bwameth'' | https://github.com/brentp/bwa-meth | The file ''bwameth'' is provided as a symbolic link to ''bwameth.py'' - you do not need to call it via Python, just ''bwameth'' is enough. |
| samtools | 2026.02+ | ''samtools'' | https://github.com/samtools/samtools | |
| sambamba | 2026.02+ | ''sambamba'' | https://github.com/biod/sambamba | |
| seqkit | 2026.02+ | ''seqkit'' | https://github.com/shenwei356/seqkit | |
| methyldackel | 2026.02+ | ''MethylDackel''\\ ''methyldackel'' | https://github.com/dpryan79/MethylDackel | The file ''methyldackel'' is provided as a symbolic link to ''MethylDackel'' for convenience / simplification of capitalisation. |
| minimap2 | 2026.02+ | ''minimap2'' | https://github.com/lh3/minimap2 | |
| bedtools2 | 2026.02+ | ''annotateBed''\\ ''bamToBed''\\ ''bamToFastq''\\ ''bed12ToBed6''\\ ''bedToBam''\\ ''bedToIgv''\\ ''bedpeToBam''\\ ''bedtools''\\ ''closestBed''\\ ''clusterBed''\\ ''complementBed''\\ ''coverageBed''\\ ''expandCols''\\ ''fastaFromBed''\\ ''flankBed''\\ ''genomeCoverageBed''\\ ''getOverlap''\\ ''groupBy''\\ ''intersectBed''\\ ''linksBed''\\ ''mapBed''\\ ''maskFastaFromBed''\\ ''mergeBed''\\ ''multiBamCov''\\ ''multiIntersectBed''\\ ''nucBed''\\ ''pairToBed''\\ ''pairToPair''\\ ''randomBed''\\ ''shiftBed''\\ ''shuffleBed''\\ ''slopBed''\\ ''sortBed''\\ ''subtractBed''\\ ''tagBam''\\ ''unionBedGraphs''\\ ''windowBed''\\ ''windowMaker'' | https://github.com/arq5x/bedtools2 | |
| bam-readcount | 2026.02+ | ''bam-readcount'' | https://github.com/genome/bam-readcount | |
| hisat2 | 2026.02+ | ''hisat2''\\ ''hisat2-align-l''\\ ''hisat2-align-s''\\ ''hisat2-inspect''\\ ''hisat2-inspect-l''\\ ''hisat2-inspect-s''\\ ''hisat2-repeat''\\ ''hisat2_extract_exons.py''\\ ''hisat2_extract_snps_haplotypes_UCSC.py''\\ ''hisat2_extract_snps_haplotypes_VCF.py''\\ ''hisat2_extract_splice_sites.py''\\ ''hisat2_read_statistics.py''\\ ''hisat2_simulate_reads.py''\\ ''extract_exons.py''\\ ''extract_splice_sites.py'' | https://cloud.biohpc.swmed.edu/index.php | |
| stringtie | 2026.02+ | ''stringtie''\\ ''prepDE.py'' | http://ccb.jhu.edu/software/stringtie/dl | |
| gffcompare | 2026.02+ | ''gffcompare''\\ ''trmap'' | http://ccb.jhu.edu/software/stringtie/dl | |
| htseq-count | 2026.02+ | ''htseq-count''\\ ''htseq-count-barcodes''\\ ''htseq-qa'' | https://pypi.org/project/HTSeq/ | The HTSeq installer places all of the files under ''/usr/local/bin'', but this is also added to the ''$PATH''. |
| picard | 2026.02+ | ''picard.jar''\\ shell alias ''picard'' | https://github.com/broadinstitute/picard/releases/download | The shell alias ''alias picard="java -jar /opt/bin/picard.jar"'' is provided to allow you to run this with the single command ''picard''. |
| seqan-library | 2026.02+ | ''alf''\\ ''bam2roi''\\ ''dfi''\\ ''fx_bam_coverage''\\ ''fx_fastq_stats''\\ ''gustaf''\\ ''gustaf_mate_joining''\\ ''insegt''\\ ''mason_frag_sequencing''\\ ''mason_genome''\\ ''mason_materializer''\\ ''mason_methylation''\\ ''mason_simulator''\\ ''mason_splicing''\\ ''mason_tests''\\ ''mason_variator''\\ ''micro_razers''\\ ''pair_align''\\ ''param_chooser''\\ ''rabema_build_gold_standard''\\ ''rabema_do_search''\\ ''rabema_evaluate''\\ ''rabema_prepare_sam''\\ ''razers''\\ ''razers3''\\ ''razers3_quality2prob''\\ ''razers3_simulate_reads''\\ ''rep_sep''\\ ''roi_feature_projection''\\ ''roi_plot_thumbnails''\\ ''s4_join''\\ ''s4_search''\\ ''sak''\\ ''sam2matrix''\\ ''samcat''\\ ''seqan_tcoffee''\\ ''seqcons2''\\ ''sgip''\\ ''splazers''\\ ''stellar''\\ ''tree_recon''\\ ''yara_indexer''\\ ''yara_mapper'' | https://github.com/seqan/seqan | These are the sample tools provided with the seqn-library installation. We have //not// installed all of the //test_// and //demo_// files. |
| regtools | 2026.02+ | ''regtools'' | https://github.com/griffithlab/regtools | |
| rseqc | 2026.02+ | All scripts as listed [[https://rseqc.sourceforge.net/#usage-information|here]] | https://rseqc.sourceforge.net | The RSeQC installer places all files in ''/usr/local/bin'' by default - this is added to ''$PATH'' so you should still be able to call ''bam2fq.py'' without giving the full path, for example. |
| Python | 2026.02+ | ''python3'' | | Currently uses version Python 3.12 |
| R | 2026.03+ | ''R'', ''Rscript'' | | Currently version 4.5.2 |
| GCC | 2026.02+ | ''gcc-14'', ''g++-14'', ''gfortran-14'' | | Please use the existing ''CFLAGS'', ''CXXFLAGS'' and ''CPPFLAGS'' environment variables which were set during the installation of the container; this will ensure the most appropriate performance optimisation flags are retained for any additional software you compile. |
**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.
----
==== Python Modules ====
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):
^ Module Name ^ Available From ^ Link ^
| HTSeq | 2026.02+ | https://htseq.readthedocs.io/en/latest/ |
| RSeQC | 2026.02+ | https://rseqc.sourceforge.net/ |
| bx_python | 2026.02+ | https://github.com/bxlab/bx-python |
| numpy | 2026.02+ | https://numpy.org/ |
| pybigwig | 2026.02+ | https://github.com/deeptools/pyBigWig |
| pysam | 2026.02+ | https://github.com/pysam-developers/pysam |
| toolshed | 2026.02+ | https://travis-ci.org/brentp/toolshed |
This list only includes modules which have been explicitly installed. The standard //Python// built-ins are still available: ''sqlite'', ''json'', etc.
----
==== R Libraries ====
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):
^ Library Name ^ Available From ^ Link ^
| AnnotationDbi | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html |
| BH | 2026.03+ | https://cran.r-project.org/web/packages/BH/index.html |
| Biobase | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/Biobase.html |
| BiocFileCache | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/BiocFileCache.html |
| BiocGenerics | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/BiocGenerics.html |
| BiocManager | 2026.03+ | https://github.com/Bioconductor/BiocManager |
| BiocParallel | 2026.03+ | https://www.bioconductor.org/packages/release/bioc/html/BiocParallel.html |
| BiocVersion | 2026.03+ | https://www.bioconductor.org/packages/release/bioc/html/BiocVersion.html |
| Biostrings | 2026.03+ | https://www.bioconductor.org/packages/release/bioc/html/Biostrings.html |
| DBI | 2026.03+ | https://cran.r-project.org/web/packages/DBI/index.html |
| DESeq2 | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| DEXSeq | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/DEXSeq.html |
| DelayedArray | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/DelayedArray.html |
| GenomicRanges | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html |
| IRanges | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/IRanges.html |
| KEGGREST | 2026.03+ | https://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html |
| MatrixGenerics | 2026.03+ | https://bioconductor.org/packages/devel/bioc/html/MatrixGenerics.html |
| R6 | 2026.03+ | https://cran.r-project.org/web/packages/R6/index.html |
| RColorBrewer | 2026.03+ | https://cran.r-project.org/web/packages/RColorBrewer/index.html |
| RSQLite | 2026.03+ | https://cran.r-project.org/web/packages/RSQLite/index.html |
| Rcpp | 2026.03+ | https://cran.r-project.org/web/packages/Rcpp/index.html |
| RcppArmadillo | 2026.03+ | https://cran.r-project.org/web/packages/RcppArmadillo/index.html |
| Rhtslib | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/Rhtslib.html |
| Rsamtools | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/Rsamtools.html |
| S4Arrays | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/S4Arrays.html |
| S4Vectors | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/S4Vectors.html |
| S7 | 2026.03+ | https://cran.r-project.org/web/packages/S7/index.html |
| Seqinfo | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/Seqinfo.html |
| SparseArray | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/SparseArray.html |
| SummarizedExperiment | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html |
| XML | 2026.03+ | https://cran.r-project.org/web/packages/XML/index.html |
| XVector | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/XVector.html |
| abind | 2026.03+ | https://cran.r-project.org/web/packages/abind/index.html |
| annotate | 2026.03+ | https://www.bioconductor.org/packages/release/bioc/html/annotate.html |
| askpass | 2026.03+ | https://cran.r-project.org/web/packages/askpass/index.html |
| biomaRt | 2026.03+ | https://bioconductor.org/packages/release/bioc/html/biomaRt.html |
| bit | 2026.03+ | https://cran.r-project.org/web/packages/bit/index.html |
| bit64 | 2026.03+ | https://cran.r-project.org/web/packages/bit64/index.html |
| bitops | 2026.03+ | https://cran.r-project.org/web/packages/bitops/index.html |
| blob | 2026.03+ | https://cran.r-project.org/web/packages/blob/index.html |
| cachem | 2026.03+ | https://cran.r-project.org/web/packages/cachem/index.html |
| cli | 2026.03+ | https://cran.r-project.org/web/packages/cli/index.html |
| cpp11 | 2026.03+ | https://cran.r-project.org/web/packages/cpp11/index.html |
| crayon | 2026.03+ | https://cran.r-project.org/web/packages/crayon/index.html |
| curl | 2026.03+ | https://cran.r-project.org/web/packages/curl/index.html |
| dbplyr | 2026.03+ | https://cran.r-project.org/web/packages/dbplyr/index.html |
| dplyr | 2026.03+ | https://cran.r-project.org/web/packages/dplyr/index.html |
| farver | 2026.03+ | https://cran.r-project.org/web/packages/farver/index.html |
| fastmap | 2026.03+ | https://cran.r-project.org/web/packages/fastmap/index.html |
| filelock | 2026.03+ | https://cran.r-project.org/web/packages/filelock/index.html |
| formatR | 2026.03+ | https://cran.r-project.org/web/packages/formatR/index.html |
| futile.logger | 2026.03+ | https://cran.r-project.org/web/packages/futile.logger/index.html |
| futile.options | 2026.03+ | https://cran.r-project.org/web/packages/futile.options/index.html |
| genefilter | 2026.03+ | https://www.bioconductor.org/packages/release/bioc/html/genefilter.html |
| geneplotter | 2026.03+ | https://www.bioconductor.org/packages/release/bioc/html/geneplotter.html |
| generics | 2026.03+ | https://cran.r-project.org/web/packages/generics/index.html |
| ggplot2 | 2026.03+ | https://cran.r-project.org/web/packages/ggplot2/index.html |
| glue | 2026.03+ | https://cran.r-project.org/web/packages/glue/index.html |
| gtable | 2026.03+ | https://cran.r-project.org/web/packages/gtable/index.html |
| hms | 2026.03+ | https://cran.r-project.org/web/packages/hms/index.html |
| httr | 2026.03+ | https://cran.r-project.org/web/packages/httr/index.html |
| httr2 | 2026.03+ | https://cran.r-project.org/web/packages/httr2/index.html |
| hwriter | 2026.03+ | https://cran.r-project.org/web/packages/hwriter/index.html |
| isoband | 2026.03+ | https://cran.r-project.org/web/packages/isoband/index.html |
| jsonlite | 2026.03+ | https://cran.r-project.org/web/packages/jsonlite/index.html |
| labeling | 2026.03+ | https://cran.r-project.org/web/packages/labeling/index.html |
| lambda.r | 2026.03+ | https://cran.r-project.org/web/packages/lambda.r/index.html |
| lifecycle | 2026.03+ | https://cran.r-project.org/web/packages/lifecycle/index.html |
| locfit | 2026.03+ | https://cran.r-project.org/web/packages/locfit/index.html |
| magrittr | 2026.03+ | https://cran.r-project.org/web/packages/magrittr/index.html |
| matrixStats | 2026.03+ | https://cran.r-project.org/web/packages/matrixStats/index.html |
| memoise | 2026.03+ | https://cran.r-project.org/web/packages/memoise/index.html |
| mime | 2026.03+ | https://cran.r-project.org/web/packages/mime/index.html |
| openssl | 2026.03+ | https://cran.r-project.org/web/packages/openssl/index.html |
| pillar | 2026.03+ | https://cran.r-project.org/web/packages/pillar/index.html |
| pkgconfig | 2026.03+ | https://cran.r-project.org/web/packages/pkgconfig/index.html |
| png | 2026.03+ | https://cran.r-project.org/web/packages/png/index.html |
| prettyunits | 2026.03+ | https://cran.r-project.org/web/packages/prettyunits/index.html |
| progress | 2026.03+ | https://cran.r-project.org/web/packages/progress/index.html |
| purrr | 2026.03+ | https://cran.r-project.org/web/packages/purrr/index.html |
| rappdirs | 2026.03+ | https://cran.r-project.org/web/packages/rappdirs/index.html |
| rlang | 2026.03+ | https://cran.r-project.org/web/packages/rlang/index.html |
| scales | 2026.03+ | https://cran.r-project.org/web/packages/scales/index.html |
| snow | 2026.03+ | https://cran.r-project.org/web/packages/snow/index.html |
| statmod | 2026.03+ | https://cran.r-project.org/web/packages/statmod/index.html |
| stringi | 2026.03+ | https://cran.r-project.org/web/packages/stringi/index.html |
| stringr | 2026.03+ | https://cran.r-project.org/web/packages/stringr/index.html |
| sys | 2026.03+ | https://cran.r-project.org/web/packages/sys/index.html |
| tibble | 2026.03+ | https://cran.r-project.org/web/packages/tibble/index.html |
| tidyr | 2026.03+ | https://cran.r-project.org/web/packages/tidyr/index.html |
| tidyselect | 2026.03+ | https://cran.r-project.org/web/packages/tidyselect/index.html |
| utf8 | 2026.03+ | https://cran.r-project.org/web/packages/utf8/index.html |
| vctrs | 2026.03+ | https://cran.r-project.org/web/packages/vctrs/index.html |
| viridisLite | 2026.03+ | https://cran.r-project.org/web/packages/viridisLite/index.html |
| withr | 2026.03+ | https://cran.r-project.org/web/packages/withr/index.html |
| xml2 | 2026.03+ | https://cran.r-project.org/web/packages/xml2/index.html |
| xtable | 2026.03+ | https://cran.r-project.org/web/packages/xtable/index.html |
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.
----
===== Building Bioapps Container =====
**Important**
This section is only relevant to RSE HPC staff or users wanting to understand how the container image is built. If you are intending to simply //use// the software you **do not** need to read this section - turn back now!
**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
#
####################################################################
%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
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 "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 \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 \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 \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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