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Releases: taffish/subread

subread v2.1.1-r2

24 May 01:19
@HermitHan HermitHan
Immutable release. Only release title and notes can be modified.
v2.1.1-r2
41ab11d

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subread v2.1.1-r2 Latest
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subread 2.1.1-r2

License metadata fix release for Subread.

Changes:

  • Corrects [package].license to Apache-2.0 for the TAFFISH app packaging.
  • Keeps the upstream license in [upstream].license: GPL-3.0-or-later.
  • Restores the app repository LICENSE file to Apache-2.0.
  • Updates the TAFFISH release, image tag, wrapper, README, help, and release notes from 2.1.1-r1 to 2.1.1-r2.
  • Does not change the packaged upstream software version or the intended command surface.

Boundaries:

  • App packaging files are Apache-2.0.
  • Upstream software and bundled components keep their own license terms.
  • Docker build logic is unchanged except for release metadata/version-text alignment where applicable.
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subread v2.1.1-r1

20 May 02:58
@HermitHan HermitHan
Immutable release. Only release title and notes can be modified.
v2.1.1-r1
e9aa267

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subread v2.1.1-r1

taf-subread 2.1.1-r1

Initial TAFFISH packaging of the SourceForge Subread command-line suite.

Changes

  • Packages official Subread 2.1.1 from the SourceForge source release, not the stale GitHub 2.0.2 release page or the GitHub master branch version marker 2.0.6.
  • Builds the C command-line suite from source and installs subread-align, subread-buildindex, subjunc, sublong, featureCounts, exactSNP, subindel, and utility commands.
  • Keeps upstream documentation, RefSeq annotation files, and test data in /opt/subread.
  • Uses a thin TAFFISH wrapper: default command is subread-align; other suite commands are exposed through command mode.

Reproducibility

  • Source tarball: https://downloads.sourceforge.net/project/subread/subread-2.1.1/subread-2.1.1-source.tar.gz
  • Source SHA256: 6392d7c66831cdd767e58251892a79a51b6fab8ed0ba9671ad5e85ff1ab01eaa
  • Runtime versions checked during image build and smoke: Subread-align v2.1.1, featureCounts v2.1.1, Subjunc v2.1.1.
  • subread-align -v prints the correct version but exits non-zero upstream; smoke validates the printed version string via a shell pipeline.
  • The Dockerfile removes the upstream -mtune=core2 compile tuning flag so the same source can compile natively for linux/amd64 and linux/arm64; this does not change the Subread version string or command surface.
  • Smoke covers command existence, version binding, help surfaces, dynamic library resolution, featureCounts on bundled SAM/GTF data, index building plus subread-align, Subjunc, and ExactSNP.

Boundaries

  • This app packages the SourceForge command-line suite only. It does not include the Bioconductor Rsubread R package or downstream R/Bioconductor differential-expression workflows.
  • Genome indexes are not bundled; users build indexes with subread-buildindex.
  • Upstream full test scripts are not used wholesale because some assume python2; small direct smoke tests use the upstream bundled test data instead.
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