Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of aviary-genome

aviary-genome - v0.12.0

- Python
Published by github-actions[bot] 11 months ago

aviary-genome - v0.11.1

- Python
Published by github-actions[bot] about 1 year ago

aviary-genome - v0.11.0

What's Changed

  • Add COMEbin as another optional binner by @AroneyS in https://github.com/rhysnewell/aviary/pull/234
  • Readd pplacer threads by @AroneyS in https://github.com/rhysnewell/aviary/pull/240
  • .gitignore: Add further aviary outputs. by @wwood in https://github.com/rhysnewell/aviary/pull/229
  • Add TaxVAMB as another optional binner by @AroneyS in https://github.com/rhysnewell/aviary/pull/244
  • Use config as env source by @AroneyS in https://github.com/rhysnewell/aviary/pull/239
  • Switch to semibin2 interface by @AroneyS in https://github.com/rhysnewell/aviary/pull/235

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.10.0...v0.11.0

- Python
Published by github-actions[bot] about 1 year ago

aviary-genome - v0.10.0

What's Changed

  • Add pyproject.toml. by @wwood in https://github.com/rhysnewell/aviary/pull/215
  • Increase base vamb runtime to 48h by @AroneyS in https://github.com/rhysnewell/aviary/pull/224
  • actions: test-aviary: Attempt fix. (#221) (for dev, last one was on main) by @wwood in https://github.com/rhysnewell/aviary/pull/225
  • config.yaml: Remove this extraneous file. by @wwood in https://github.com/rhysnewell/aviary/pull/220
  • spades: Update to 4. by @wwood in https://github.com/rhysnewell/aviary/pull/216
  • Fix vamb being excluded from dastool by @AroneyS in https://github.com/rhysnewell/aviary/pull/227
  • aviary: Update --build help message. by @wwood in https://github.com/rhysnewell/aviary/pull/222
  • assemble/recover: Require users to specify coassembly or not. by @wwood in https://github.com/rhysnewell/aviary/pull/223

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.9.2...v0.10.0

- Python
Published by github-actions[bot] over 1 year ago

aviary-genome - v0.9.2

What's Changed

  • chore: Update CITATION.cff by @rhysnewell in https://github.com/rhysnewell/aviary/pull/197
  • Fix checkm2 env by @AroneyS in https://github.com/rhysnewell/aviary/pull/212
  • Update annotation.smkwith new GTDB DB URL by @JamesRH in https://github.com/rhysnewell/aviary/pull/207

New Contributors

  • @JamesRH made their first contribution in https://github.com/rhysnewell/aviary/pull/207

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.9.1...v0.9.2

- Python
Published by github-actions[bot] over 1 year ago

aviary-genome - v0.9.1

What's Changed

  • fix: batch submission now does not require user to write to script first by @rhysnewell in https://github.com/rhysnewell/aviary/pull/199
  • fix: batch checks read type correctly by @rhysnewell in https://github.com/rhysnewell/aviary/pull/202
  • convert rule spades_assembly to a python script by @YibiChen in https://github.com/rhysnewell/aviary/pull/201
  • fix tmpdir being set from base command by @AroneyS in https://github.com/rhysnewell/aviary/pull/200

New Contributors

  • @YibiChen made their first contribution in https://github.com/rhysnewell/aviary/pull/201

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.9.0...v0.9.1

- Python
Published by github-actions[bot] almost 2 years ago

aviary-genome - v0.9.0

What's Changed

  • megahit: Specify -m in bytes. by @wwood in https://github.com/rhysnewell/aviary/pull/176
  • cff-update: Update to v0.8.3. by @wwood in https://github.com/rhysnewell/aviary/pull/175
  • singlem: Update to 0.16.0. by @wwood in https://github.com/rhysnewell/aviary/pull/177
  • Add SingleM metapackage downloading by @AroneyS in https://github.com/rhysnewell/aviary/pull/173
  • threading issues and rosella version by @rhysnewell in https://github.com/rhysnewell/aviary/pull/179
  • das_tool: Use script not shell. by @wwood in https://github.com/rhysnewell/aviary/pull/187
  • Loosen same-group permissions for folders and logs by @AroneyS in https://github.com/rhysnewell/aviary/pull/189
  • Doco updates by @wwood in https://github.com/rhysnewell/aviary/pull/184
  • Adding binning-only flag, simplify recipes by @rhysnewell in https://github.com/rhysnewell/aviary/pull/192

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.8.3...v0.9.0

- Python
Published by github-actions[bot] almost 2 years ago

aviary-genome - v0.8.3

What's Changed

  • v0.8.2 by @rhysnewell in https://github.com/rhysnewell/aviary/pull/160
  • attempt to fix #166 by interleaving reads correctly by @rhysnewell in https://github.com/rhysnewell/aviary/pull/167
  • Singlem update by @wwood in https://github.com/rhysnewell/aviary/pull/156
  • Set pplacer threads by @AroneyS in https://github.com/rhysnewell/aviary/pull/171
  • citations: Improve them. by @wwood in https://github.com/rhysnewell/aviary/pull/162
  • Update rosella to v0.5.0 by @rhysnewell in https://github.com/rhysnewell/aviary/pull/168

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.8.2...v0.8.3

- Python
Published by github-actions[bot] over 2 years ago

aviary-genome - v0.8.2

What's Changed

  • Fix arg parsing issue by @rhysnewell in https://github.com/rhysnewell/aviary/pull/144
  • Update resources by @AroneyS in https://github.com/rhysnewell/aviary/pull/153
  • Fix short read coassemble qc by @AroneyS in https://github.com/rhysnewell/aviary/pull/155
  • Add fastp and update docs by @rhysnewell in https://github.com/rhysnewell/aviary/pull/154
  • singlem: Restrict to 0.13.2. Fixes #157. by @wwood in https://github.com/rhysnewell/aviary/pull/159

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.8.1...v0.8.2

- Python
Published by github-actions[bot] over 2 years ago

aviary-genome - v0.8.1

What's Changed

  • bump to v0.8.0 by @rhysnewell in https://github.com/rhysnewell/aviary/pull/141

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.8.0...v0.8.1

- Python
Published by github-actions[bot] over 2 years ago

aviary-genome - v0.8.0

What's Changed

  • update deploy docs by @rhysnewell in https://github.com/rhysnewell/aviary/pull/116
  • v0.7.1 by @rhysnewell in https://github.com/rhysnewell/aviary/pull/119
  • bump version by @rhysnewell in https://github.com/rhysnewell/aviary/pull/125
  • v0.7.2 by @rhysnewell in https://github.com/rhysnewell/aviary/pull/126
  • fix empty bin_info.tsv with --skip-abundances by @AroneyS in https://github.com/rhysnewell/aviary/pull/127
  • Catchup dev to main by @AroneyS in https://github.com/rhysnewell/aviary/pull/128
  • Better snakemake cluster submission support by @AroneyS in https://github.com/rhysnewell/aviary/pull/129
  • Remove upper snakemake bound by @AroneyS in https://github.com/rhysnewell/aviary/pull/131
  • Make long read qc temp by @rhysnewell in https://github.com/rhysnewell/aviary/pull/132
  • fix: link reads was not properly account for coassemble flag by @rhysnewell in https://github.com/rhysnewell/aviary/pull/139

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.7.2...v0.8.0

- Python
Published by github-actions[bot] over 2 years ago

aviary-genome - v0.7.2

What's Changed

  • refinery: only copy actual bins by @AroneyS in https://github.com/rhysnewell/aviary/pull/121
  • Implement skip abundances arg by @AroneyS in https://github.com/rhysnewell/aviary/pull/123

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.7.1...v0.7.2

- Python
Published by github-actions[bot] over 2 years ago

aviary-genome - v0.7.1

What's Changed

  • Citations update by @wwood in https://github.com/rhysnewell/aviary/pull/109
  • update: v0.7.0 by @rhysnewell in https://github.com/rhysnewell/aviary/pull/110
  • Merge v0.7.0 to main by @rhysnewell in https://github.com/rhysnewell/aviary/pull/111
  • update: documentation branch from master to main by @rhysnewell in https://github.com/rhysnewell/aviary/pull/112
  • update: docs workflow by @rhysnewell in https://github.com/rhysnewell/aviary/pull/113
  • Update docs changes so they also occur on dev branch by @rhysnewell in https://github.com/rhysnewell/aviary/pull/114
  • add: homebrew setup in actions by @rhysnewell in https://github.com/rhysnewell/aviary/pull/115
  • fixed combine assembly script, fixes #117 by @rhysnewell in https://github.com/rhysnewell/aviary/pull/118

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.7.0...v0.7.1

- Python
Published by github-actions[bot] over 2 years ago

aviary-genome - v0.7.0

What's Changed

  • Merge Dev into Main by @rhysnewell in https://github.com/rhysnewell/aviary/pull/96
  • update version to v0.6.0 on main by @rhysnewell in https://github.com/rhysnewell/aviary/pull/98
  • Rework skip-binners by @AroneyS in https://github.com/rhysnewell/aviary/pull/101
  • Catch dev up to main by @rhysnewell in https://github.com/rhysnewell/aviary/pull/102
  • Add refinery max iterations arg by @AroneyS in https://github.com/rhysnewell/aviary/pull/103
  • Update to semibin2 by @AroneyS in https://github.com/rhysnewell/aviary/pull/104
  • Fix checkm subprocess by @AroneyS in https://github.com/rhysnewell/aviary/pull/105
  • fix: removal of instances of shell=True by @rhysnewell in https://github.com/rhysnewell/aviary/pull/107

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.6.0...v0.7.0

- Python
Published by github-actions[bot] over 2 years ago

aviary-genome - v0.6.0

What's Changed

  • fix: closes #82 fix typo on rerun_triggers by @rhysnewell in https://github.com/rhysnewell/aviary/pull/83
  • Merge Dev, close #84 by @rhysnewell in https://github.com/rhysnewell/aviary/pull/85
  • Fixes #87, argparse input long-read-type as string not list by @rhysnewell in https://github.com/rhysnewell/aviary/pull/88
  • Merge main into dev by @rhysnewell in https://github.com/rhysnewell/aviary/pull/95
  • Merge Medaka into Dev by @rhysnewell in https://github.com/rhysnewell/aviary/pull/97

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.5.7...v0.6.0

- Python
Published by github-actions[bot] over 2 years ago

aviary-genome - v0.5.7

Fixes #87

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.5.5...v0.5.7

- Python
Published by github-actions[bot] about 3 years ago

aviary-genome - v0.5.6

What's Changed

  • Fix paired end reads mismatching by @AroneyS in https://github.com/rhysnewell/aviary/pull/80
  • fix: closes #82 fix typo on rerun_triggers by @rhysnewell in https://github.com/rhysnewell/aviary/pull/83
  • Merge Dev, close #84 by @rhysnewell in https://github.com/rhysnewell/aviary/pull/85

New Contributors

  • @AroneyS made their first contribution in https://github.com/rhysnewell/aviary/pull/80

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.5.4...v0.5.6

- Python
Published by github-actions[bot] over 3 years ago

aviary-genome - v0.5.5 - Broken

What's Changed

  • Fix paired end reads mismatching by @AroneyS in https://github.com/rhysnewell/aviary/pull/80

New Contributors

  • @AroneyS made their first contribution in https://github.com/rhysnewell/aviary/pull/80

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.5.4...v0.5.5

- Python
Published by github-actions[bot] over 3 years ago

aviary-genome - v0.5.4

- Python
Published by github-actions[bot] over 3 years ago

aviary-genome - v0.5.0

Full Changelog: https://github.com/rhysnewell/aviary/compare/v0.4.3...v0.5.0

- Python
Published by github-actions[bot] over 3 years ago

aviary-genome - v0.4.3

Bug Fixes

  • cluster now compatible with checkm1 and 2 scores, fix singlem yaml (Rhys Newell)
  • skip binners even if assembly is constructed. Complete now includes bin_info steps (Rhys Newell)
  • singlem error causes pipeline crash, closes #61 (Rhys Newell)

Commits

  • 80dc5b6: fix release portion of github actions (Rhys Newell)
  • 1f993fe: add use of checkm2 cmd line param (Rhys Newell)
  • b216049: various cluster fixes, default min completeness and max con now empty (Rhys Newell)
  • d5816d8: closes #61, binners should no longer be initialized if skipped when assembly is created. Complete workflow targets correct recover output (Rhys Newell)
  • taxonomy now included in bin_info.tsv (Rhys Newell)
  • pangenome analysis pipeline within cluster (Rhys Newell)

- Python
Published by github-actions[bot] over 3 years ago

aviary-genome - v0.4.1

Messing around with bioconda recipe. Imports not working on bioconda?

- Python
Published by rhysnewell over 3 years ago

aviary-genome - v0.4.0

v0.4.0 - more flexibility during binning!

  • Ability to skip binners using --skip-binners flag
  • SemiBin now included as optional binning algorithim. Currently skipped by default, this may change in future
  • Improved MAG metadata information:
    • Checkm1 out_format 2 now included
    • MAG circularity information
  • General stability improvements - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - N.B. Old installs might require conda envs to be rebuilt. Strict channel priority ordering is now enforced by snakemake so yaml files had to be updated - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

- Python
Published by rhysnewell over 3 years ago

aviary-genome - v0.3.0

Adding cluster submodule for combining and dereplicating bins across multiple aviary runs using galah

- Python
Published by rhysnewell about 4 years ago

aviary-genome - v0.1.1

Adding usage for mamba over conda Modularized assembly and binning - Simple assembly command added for short reads Defaulting to not using vamb due to speed issues. Adding need for GTDBTKDATAPATH and CONDAENVPATH to be set by users or use respective command line flags

- Python
Published by rhysnewell almost 5 years ago

aviary-genome - v0.1.0

First release, just the binning pipeline + singleM. updates will follow

- Python
Published by rhysnewell almost 5 years ago