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BioContainers

BioContainers is a community project using container technology to package bioinformatics software. Find more about BioContainers at https://biocontainers.pro

Getting Started​

Listing Available BioContainers​

On Palmetto, start by running module load biocontainers. Now, run module avail to view the list the current BioContainers downloaded on Palmetto.

[user@node1234 ~]$ module load biocontainers
[user@node1234 ~]$ module avail

------------------------------------------------------------------------------------- /software/containers/biocontainers/modules --------------------------------------------------------------------------------------
   bcftools/1.17    bwa/v0.7.17      gatk4/4.2.6.0    interproscan/5.59-91.0    picard/3.0.0     repeatmasker/4.1.5     skewer/0.1.126     subread/2.0.6        vcftools/v0.1.16
   blast/2.14.0     cutadapt/4.4     hisat2/2.2.1     jellyfish/1.1.12          prokka/1.14.6    repeatmodeler/2.0.4    spades/3.15.5      trim-galore/0.6.9    vsearch/2.23.0
   bowtie2/2.5.1    diamond/2.1.8    hmmer/3.3.2      multiqc/1.13a             qiime2/2023.5    rsem/1.3.3             sra-tools/3.0.6    trimmomatic/0.35
   busco/5.4.7      fastqc/0.12.1    htseq/2.0.3      muscle/5.1                quast/5.2.0      samtools/1.17          star/2.7.10b       trinity/2.15.1

Loading Modules​

You can load the modules with:

module load biocontainers
module load qiime2

or

ml biocontainers qiime2
note

The above statements are functionally identical

Using the Container​

Now that a module is loaded, you can run the command as normal:

[user@node1234 ~]$ ml biocontainers qiime2
[user@node1234 ~]$ qiime info
System versions
Python version: 3.8.16
QIIME 2 release: 2023.5
QIIME 2 version: 2023.5.1
q2cli version: 2023.5.1

Installed plugins
alignment: 2023.5.0
composition: 2023.5.0
cutadapt: 2023.5.1
dada2: 2023.5.0
deblur: 2023.5.0
demux: 2023.5.0
diversity: 2023.5.1
diversity-lib: 2023.5.0
emperor: 2023.5.0
feature-classifier: 2023.5.0
feature-table: 2023.5.0
fragment-insertion: 2023.5.0
gneiss: 2023.5.0
longitudinal: 2023.5.0
metadata: 2023.5.0
phylogeny: 2023.5.0
quality-control: 2023.5.0
quality-filter: 2023.5.0
sample-classifier: 2023.5.0
taxa: 2023.5.0
types: 2023.5.0
vsearch: 2023.5.0

Application config directory
/home/qiime2/q2cli

Getting help
To get help with QIIME 2, visit https://qiime2.org
[user@node1234 ~]$

Accessing Palmetto Filesystems​

Running a biocontainer mounts $PWD and $TMPDIR inside the container along with $HOME. If you need to access a different filesystem, set the $APPTAINER_BINDPATH environment variable.

Example​

If your current $PWD is in /project/tiger/mylab, and you want to mount /scratch/$USER

export APPTAINER_BINDPATH="/scratch"

The program running inside the container will now have access to the /scratch filesystem for reading and writing.

Requesting a new module​

There are thousands of biocontainers available. If you would like one added to Palmetto please use the Palmetto Software Request page.

Learning the tools​

We provide additional documentation on all the tools we provide in the biocontainer tools section