Using Apptainer to Run BLAST+
Last updated on 2026-10-06 | Edit this page
Estimated time: 60 minutes
Overview
Questions
- How can I use Apptainer to run bioinformatics workflows with BLAST+?
Objectives
- Show example of using Apptainer with a common bioinformatics tool.
We have now learned enough to be able to use Apptainer to deploy software on a remote HPC system without us needing to install the software itself on the host system.
In this section we will demonstrate the use of an Apptainer container image that provides the BLAST+ bioinformatics software. The BLAST+ suite of software tools is typically complex to install from source by hand on a HPC system. Using containers we are able to avoid this complexity and get up and running with the software quickly.
Source material
This example is based on the example from the official NCBI
BLAST+ Docker container documentation Note: the efetch
parts of the step-by-step guide do not currently work using Apptainer
version of the image so we provide a dataset with the data already
downloaded.
(This is because the NCBI BLAST+ Docker container image has the
efetch tool installed in the /root directory
and this special location gets overwritten during the conversion to a
Apptainer container image.)
Download the required data
Download the blast_example.tar.gz.
Unpack the archive which contains the downloaded data required for the BLAST+ example:
BASH
remote$ wget https://github.com/EPCCed/2026-10-07_podman-apptainer_imperial/raw/refs/heads/main/episodes/files/blast_example.tar.gz
remote$ tar -xvf blast_example.tar.gzOUTPUT
x blast/
x blast/blastdb/
x blast/queries/
x blast/fasta/
x blast/results/
x blast/blastdb_custom/
x blast/fasta/nurse-shark-proteins.fsa
x blast/queries/P01349.fsaFinally, move into the newly created directory:
OUTPUT
blastdb blastdb_custom fasta queries resultsCreate the Apptainer container image
NCBI provide official Docker containers with the BLAST+ software hosted on Docker Hub. We can create an Apptainer container image from the Docker container image with:
OUTPUT
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
INFO: Fetching OCI image...
29.0MiB / 29.0MiB [=========================================================================================================================================================================] 100 % 22.2 MiB/s 0s
14.8MiB / 14.8MiB [=========================================================================================================================================================================] 100 % 22.2 MiB/s 0s
50.4MiB / 50.4MiB [=========================================================================================================================================================================] 100 % 22.2 MiB/s 0s
448.8KiB / 448.8KiB [=======================================================================================================================================================================] 100 % 22.2 MiB/s 0s
40.9MiB / 40.9MiB [=========================================================================================================================================================================] 100 % 22.2 MiB/s 0s
150.7MiB / 150.7MiB [=======================================================================================================================================================================] 100 % 22.2 MiB/s 0s
22.7MiB / 22.7MiB [=========================================================================================================================================================================] 100 % 22.2 MiB/s 0s
49.1MiB / 49.1MiB [=========================================================================================================================================================================] 100 % 22.2 MiB/s 0s
INFO: Extracting OCI image...
INFO: Inserting Apptainer configuration...
INFO: Creating SIF file...
[======================================================================================================================================================================================================] 100 % 0sNow we have a container with the software in, we can use it.
Build and verify the BLAST database
Our example dataset has already downloaded the query and database
sequences. We first use these downloaded data to create a custom BLAST
database by using a container to run the command
makeblastdb with the correct options.
BASH
remote$ apptainer exec --cleanenv ncbi-blast.sif \
makeblastdb -in fasta/nurse-shark-proteins.fsa -dbtype prot \
-parse_seqids -out nurse-shark-proteins -title "Nurse shark proteins" \
-taxid 7801 -blastdb_version 5OUTPUT
Building a new DB, current time: 10/06/2026 14:05:20
New DB name: /home/auser/test/blast/blast/nurse-shark-proteins
New DB title: Nurse shark proteins
Sequence type: Protein
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 7 sequences in 0.021101 seconds.
## --cleanenv option
By default, Apptainer makes sure most of your host environment
settings are available in the running container. Full details of what
Apptainer does are
available in the User Guide. However, this can cause compatibility
problems so it is often best to start in the running container with a
clean environment and only add environment settings as needed. The
--cleanenv option to Apptainer tells the running container
to not take environment settings from the host.
To verify the newly created BLAST database above, you can run the
blastdbcmd -entry all -db nurse-shark-proteins -outfmt "%a %l %T"
command to display the accessions, sequence length, and common name of
the sequences in the database.
BASH
remote$ apptainer exec --cleanenv ncbi-blast.sif \
blastdbcmd -entry all -db nurse-shark-proteins -outfmt "%a %l %T"OUTPUT
Q90523.1 106 7801
P80049.1 132 7801
P83981.1 53 7801
P83977.1 95 7801
P83984.1 190 7801
P83985.1 195 7801
P27950.1 151 7801Now we have our database we can run queries against it.
Run a query against the BLAST database
Lets execute a query on our database using the blastp
command:
BASH
remote$ apptainer exec --cleanenv ncbi-blast.sif \
blastp -query queries/P01349.fsa -db nurse-shark-proteins \
-out results/blastp.outAt this point, you should see the results of the query in the output
file results/blastp.out. To view the content of this output
file, use the command less results/blastp.out.
OUTPUT
...output trimmed...
Query= sp|P01349.2|RELX_CARTA RecName: Full=Relaxin; Contains: RecName:
Full=Relaxin B chain; Contains: RecName: Full=Relaxin A chain
Length=44
Score E
Sequences producing significant alignments: (Bits) Value
P80049.1 RecName: Full=Fatty acid-binding protein, liver; AltName... 14.2 0.96
>P80049.1 RecName: Full=Fatty acid-binding protein, liver; AltName: Full=Liver-type
fatty acid-binding protein; Short=L-FABP
Length=132
...output trimmed...With your query, BLAST identified the protein sequence P80049.1 as a match with a score of 14.2 and an E-value of 0.96.
Accessing online BLAST databases
As well as building your own local database to query, you can also access databases that are available online. For example, to see which databases are available online in the Google Compute Platform (GCP):
BASH
remote$ apptainer exec --cleanenv ncbi-blast.sif update_blastdb.pl --showall pretty --source gcpOUTPUT
Connected to GCP
BLASTDB DESCRIPTION SIZE (GB) LAST_UPDATED
nr All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects 753.9510 2026-09-27
swissprot Non-redundant UniProtKB/SwissProt sequences 0.3659 2026-09-15
refseq_protein NCBI Protein Reference Sequences 257.3614 2026-08-27
landmark Landmark database for SmartBLAST 0.4693 2025-08-06
pdbaa PDB protein database 0.2615 2026-09-29
nt Nucleotide collection (nt) 1199.4928 2026-09-24
core_nt Core nucleotide BLAST database 301.4805 2026-09-19
pdbnt PDB nucleotide database 0.0155 2026-09-24
patnt Nucleotide sequences derived from the Patent division of GenBank 19.2072 2026-09-19
refseq_rna NCBI Transcript Reference Sequences 80.1543 2026-09-16
...output trimmed...Similarly, for databases hosted at NCBI:
BASH
remote$ apptainer exec --cleanenv ncbi-blast.sif update_blastdb.pl --showall pretty --source ncbiOUTPUT
Connected to NCBI
BLASTDB DESCRIPTION SIZE (GB) LAST_UPDATED
18S_fungal_sequences 18S ribosomal RNA sequences (SSU) from Fungi type and reference material 0.0026 2026-10-03
Betacoronavirus Betacoronavirus 71.0289 2025-06-26
28S_fungal_sequences 28S ribosomal RNA sequences (LSU) from Fungi type and reference material 0.0072 2026-10-03
16S_ribosomal_RNA 16S ribosomal RNA (Bacteria and Archaea type strains) 0.0184 2026-10-03
ITS_RefSeq_Fungi Internal transcribed spacer region (ITS) from Fungi type and reference material 0.0091 2026-10-05
ITS_eukaryote_sequences ITS eukaryote BLAST 0.0344 2026-10-05
LSU_eukaryote_rRNA Large subunit ribosomal nucleic acid for Eukaryotes 0.0053 2022-12-05
LSU_prokaryote_rRNA Large subunit ribosomal nucleic acid for Prokaryotes 0.0041 2022-12-05
SSU_eukaryote_rRNA Small subunit ribosomal nucleic acid for Eukaryotes 0.0063 2022-12-05
env_nt environmental samples 0.4413 2026-09-16
env_nr Proteins from WGS metagenomic projects (env_nr). 4.4552 2026-09-30
...output trimmed...Notes
You have now completed a simple example of using a complex piece of bioinformatics software through Apptainer containers. You may have noticed that some things just worked without you needing to set them up even though you were running using containers:
- We did not need to explicitly bind any files/directories in to the container. This worked because Apptainer automatically binds the current directory into the running container, so any data in the current directory (or its subdirectories) will generally be available in running Apptainer containers. (Note, this is different from the behaviour of the Podman containers we were using earlier in this workshop.)
- Access to the internet is automatically available within the running container in the same way as it is on the host system without us needed to specify any additional options.
- Files and data we create within the container have the right ownership and permissions for us to access outside the container.
In addition, we were able to use the tools in the container image provided by NCBI without having to do any work to install the software irrespective of the computing platform that we are using. (In fact, the example this is based on runs the pipeline using Docker on a cloud computing platform rather than on your local system.)
- We can use containers to run software without having to install it
- The commands we use are very similar to those we would use natively
- Apptainer handles a lot of complexity around data and internet access for us
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