bustools v0.45.1-r2

Publish bustools 0.45.1-r2 as a TAFFISH app

This release updates the TAFFISH packaging for bustools 0.45.1. The upstream
bustools version and container build recipe are unchanged from r1; r2 corrects
the TAFFISH command-mode documentation so users call bustools subcommands
through the in-container bustools executable.

Package

• Package: bustools
• Command: taf-bustools
• Version: 0.45.1-r2
• Container image: ghcr.io/taffish/bustools:0.45.1-r2
• Upstream project: bustools

Installation

After the release is indexed by TAFFISH Hub, users can install it with:

taf update
taf install bustools

The exact release can also be requested with:

taf install bustools 0.45.1-r2

User Interface

• Provides taf-bustools as the TAFFISH entry point for bustools.
• Keeps the standard thin <taf-app> wrapper:
  bustools ::*ARGV*::.
• Documents taf-bustools bustools <SUBCOMMAND> ... as the required form for
  upstream bustools subcommands such as sort, count, and inspect.
• Clarifies that taf-bustools sort ... is not correct in TAFFISH command mode,
  because the first non-option argument is treated as an in-container
  executable.
• Supports upstream command summary, version, and citation paths.
• Documents common manual workflow steps: inspect, correct, sort, and
  count.
• Documents BUS text conversion, BUSZ compression, and decompression examples.
• Clarifies that kallisto and kb-python are broader workflow tools and are not
  bundled in this focused bustools app.

Container

• Uses debian:12-slim as the base image.
• Downloads the official upstream v0.45.1 source archive from GitHub.
• Builds bustools from source with CMake, GCC/G++, Make, and zlib development
  headers in a builder stage.
• Installs only the compiled bustools binary into the runtime image.
• Keeps runtime dependencies minimal: libstdc++6 and zlib1g.
• Supports linux/amd64 and linux/arm64.

Trust And Smoke Checks

• Adds TAFFISH smoke metadata in taffish.toml.
• Checks that bustools is available in the container PATH.
• Requires bustools version to report upstream version 0.45.1.
• Checks command summary and citation output.
• Checks common subcommand help paths, including sort, correct, count,
  inspect, allowlist, capture, text, fromtext, extract,
  umicorrect, compress, and decompress.
• Checks extended upstream subcommands and aliases, including project,
  linker, collapse, clusterhist, predict, merge, mash, inflate,
  dump, and whitelist.
• Runs a tiny functional round-trip that converts tab-delimited text to BUS
  with fromtext, then converts the BUS file back to text with text.
• Keeps the container image tag aligned with the TAFFISH package version
  0.45.1-r2.

Validation Notes

Before publishing, build and test the image locally:

taf check
docker build -t ghcr.io/taffish/bustools:0.45.1-r2 -f docker/Dockerfile .
docker run --rm ghcr.io/taffish/bustools:0.45.1-r2 bustools version
docker run --rm ghcr.io/taffish/bustools:0.45.1-r2 bustools sort

For cross-platform validation, build at least the supported local target and
one explicit amd64 target:

docker build -t taffish-bustools:local -f docker/Dockerfile .
docker build --platform linux/amd64 -t taffish-bustools:amd64-local -f docker/Dockerfile .

The smoke metadata also verifies the published image during TAFFISH Hub
indexing.

License

The repository wrapper files are Apache-2.0. Upstream bustools is distributed
under the BSD-2-Clause license, and third-party runtime components are
distributed under their own upstream licenses.

Citation

• Melsted et al. 2021, Modular, efficient and constant-memory single-cell
  RNA-seq preprocessing, doi:10.1038/s41587-021-00870-2, PMID:33795888.
• Melsted et al. 2019, The Barcode, UMI, Set format and BUStools,
  doi:10.1093/bioinformatics/btz279.

bustools v0.45.1-r1

Publish bustools 0.45.1 as a TAFFISH app

This release packages bustools 0.45.1 as a TAFFISH tool app for manipulating
BUS files from single-cell RNA-seq workflows through the versioned
taf-bustools command.

Package

• Package: bustools
• Command: taf-bustools
• Version: 0.45.1-r1
• Container image: ghcr.io/taffish/bustools:0.45.1-r1
• Upstream project: bustools

Installation

After the release is indexed by TAFFISH Hub, users can install it with:

taf update
taf install bustools

The exact release can also be requested with:

taf install bustools 0.45.1-r1

User Interface

• Provides taf-bustools as the TAFFISH entry point for bustools.
• Forwards subcommands and options directly to the upstream bustools binary.
• Supports upstream command summary, version, and citation paths.
• Documents common manual workflow steps: inspect, correct, sort, and
  count.
• Documents BUS text conversion, BUSZ compression, and decompression examples.
• Clarifies that kallisto and kb-python are broader workflow tools and are not
  bundled in this focused bustools app.

Container

• Uses debian:12-slim as the base image.
• Downloads the official upstream v0.45.1 source archive from GitHub.
• Builds bustools from source with CMake, GCC/G++, Make, and zlib development
  headers in a builder stage.
• Installs only the compiled bustools binary into the runtime image.
• Keeps runtime dependencies minimal: libstdc++6 and zlib1g.
• Supports linux/amd64 and linux/arm64.

Trust And Smoke Checks

• Adds TAFFISH smoke metadata in taffish.toml.
• Checks that bustools is available in the container PATH.
• Requires bustools version to report upstream version 0.45.1.
• Checks command summary and citation output.
• Checks common subcommand help paths, including sort, correct, count,
  inspect, allowlist, capture, text, fromtext, extract,
  umicorrect, compress, and decompress.
• Checks extended upstream subcommands and aliases, including project,
  linker, collapse, clusterhist, predict, merge, mash, inflate,
  dump, and whitelist.
• Runs a tiny functional round-trip that converts tab-delimited text to BUS
  with fromtext, then converts the BUS file back to text with text.
• Keeps the container image tag aligned with the TAFFISH package version
  0.45.1-r1.

Validation Notes

Before publishing, build and test the image locally:

taf check
docker build -t ghcr.io/taffish/bustools:0.45.1-r1 -f docker/Dockerfile .
docker run --rm ghcr.io/taffish/bustools:0.45.1-r1 bustools version
docker run --rm ghcr.io/taffish/bustools:0.45.1-r1 bustools sort

Cross-platform validation was performed locally for both supported image
targets:

docker build -t taffish-bustools:local -f docker/Dockerfile .
docker build --platform linux/amd64 -t taffish-bustools:amd64-local -f docker/Dockerfile .

The smoke metadata also verifies the published image during TAFFISH Hub
indexing.

License

The repository wrapper files are Apache-2.0. Upstream bustools is distributed
under the BSD-2-Clause license, and third-party runtime components are
distributed under their own upstream licenses.

Citation

• Melsted et al. 2021, Modular, efficient and constant-memory single-cell
  RNA-seq preprocessing, doi:10.1038/s41587-021-00870-2, PMID:33795888.
• Melsted et al. 2019, The Barcode, UMI, Set format and BUStools,
  doi:10.1093/bioinformatics/btz279.