taf-qualimap

TAFFISH wrapper for Qualimap 2.3, a Java/R application for quality control of high-throughput sequencing alignments and derived count data.

Package Identity

field	value
name	qualimap
command	taf-qualimap
version	2.3-r1
kind	tool
image	ghcr.io/taffish/qualimap:2.3-r1
upstream	Qualimap 2.3 official ZIP
runtime version	QualiMap v.2.3, built 2023-05-19

Installation

taf install qualimap

You can also run a versioned wrapper after publishing or local build:

taf-qualimap --help
taf-qualimap --version

CLI Use

Qualimap's own command line follows:

qualimap <tool_name> <tool_options>

Because this is a TAFFISH taf-app with command mode, the recommended form is to name the upstream command explicitly:

taf-qualimap qualimap bamqc -bam sample.bam -outdir sample_bamqc
taf-qualimap qualimap rnaseq -bam rnaseq.bam -gtf genes.gtf -outdir rnaseq_qc
taf-qualimap qualimap counts -d counts_design.tsv -outdir counts_qc
taf-qualimap qualimap multi-bamqc -d reports.tsv -outdir multi_bamqc

To pass option-leading arguments to the default upstream command:

taf-qualimap -- --help

Qualimap does not provide a clean separate --version command. The upstream version banner is checked through qualimap --help and reports QualiMap v.2.3.

Packaged Qualimap Tools

This image exposes the official Qualimap launcher and preserves the upstream tool names:

tool	purpose
bamqc	QC for SAM/BAM alignments
rnaseq	RNA-seq alignment QC using a GTF annotation
counts	counts table QC
multi-bamqc	comparison of multiple BAM QC reports
clustering	epigenomic signal clustering
comp-counts	compute feature counts from alignments and GTF

The image includes OpenJDK 17, R, Debian-packaged R dependencies, and the archived gsmoothr/Repitools packages needed by Qualimap's GUI and legacy clustering checks. The upstream launcher is patched only to remove the obsolete Java MaxPermSize VM option, which modern OpenJDK rejects.

GUI Mode

Qualimap also has a Java GUI. In TAFFISH, the command-line interface remains the default reproducible surface, and GUI mode is provided by the helper qualimap-gui.

Start a temporary noVNC session with Docker:

TAFFISH_CONTAINER_BACKEND=docker \
TAFFISH_DOCKER_RUN_ARGS="-p 127.0.0.1:5801:5801" \
taf-qualimap qualimap-gui

The helper prints the browser URL when it starts:

http://127.0.0.1:5801/vnc.html?autoconnect=1&resize=scale

Podman is similar:

TAFFISH_CONTAINER_BACKEND=podman \
TAFFISH_PODMAN_RUN_ARGS="-p 127.0.0.1:5801:5801" \
taf-qualimap qualimap-gui

If host port 5801 is occupied, keep the container port at 5801 and change the host port plus the printed URL hint:

TAFFISH_DOCKER_RUN_ARGS="-p 127.0.0.1:5802:5801" \
taf-qualimap qualimap-gui --host-port 5802

For a remote server, create an SSH tunnel first:

ssh -L 5801:127.0.0.1:5801 user@server

Then open the same localhost URL in your local browser. Press Ctrl-C in the terminal to stop the GUI session; Docker and Podman runs embed --init for more predictable child-process cleanup.

Useful GUI helper options:

--geometry WxH        virtual screen size, default 1280x800
--port PORT           noVNC HTTP port inside the container, default 5801
--host-port PORT      host port shown in the printed URL
--java-mem-size SIZE  Java heap size passed to Qualimap
--password PASS       require a VNC password

The default examples bind the host port to 127.0.0.1. Do not expose the noVNC port to a shared network unless you add --password or put it behind site-level access control. noVNC is served over plain HTTP in the container.

Platform Notes

Qualimap's official 2.3 ZIP is platform-independent Java/R code. This app is intended to build native images for both linux/amd64 and linux/arm64.

GUI mode is best supported with Docker or Podman because it needs a long-running HTTP port and VNC session. Apptainer GUI behavior is site-dependent. CLI mode is the primary reproducible mode.

Boundaries

Qualimap's official manual lists several R/Bioconductor packages. Most R runtime dependencies used by this image come from Debian 12 packages, including NOISeq, Rsamtools, GenomicFeatures, and rtracklayer.

gsmoothr and Repitools are installed from fixed source tarballs with checksum verification because Repitools is not packaged in Debian 12. This avoids the GUI startup warning about missing R packages and keeps the upstream clustering entry available. The smoke suite verifies package imports and small report paths, but full scientific validation of real clustering analyses remains a dataset-level responsibility.

Smoke Coverage

The release smoke checks:

• upstream Qualimap 2.3 banner and public tool help
• Java and R runtime availability
• R package imports for the packaged Qualimap report dependencies
• a minimal SAM alignment through qualimap bamqc
• a minimal two-sample report through qualimap multi-bamqc
• a minimal counts table through qualimap counts
• qualimap-gui help and noVNC startup

The smoke is deliberately small. It verifies container functionality and basic runtime dependencies, not scientific interpretation of real datasets.

Upstream And Citation

• Homepage: http://qualimap.conesalab.org/
• Manual: http://qualimap.conesalab.org/doc_html/index.html
• Download: https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip
• License: GPL-2.0-only

If you use Qualimap 2, cite:

Okonechnikov, K., Conesa, A., & García-Alcalde, F. (2016). Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. DOI: 10.1093/bioinformatics/btv566; PMID: 26428292.

The original Qualimap paper is:

García-Alcalde et al. (2012). Qualimap: evaluating next generation sequencing alignment data. Bioinformatics. DOI: 10.1093/bioinformatics/bts503; PMID: 22914218.