Releases | Open Source Science

binchicken - v0.13.4

Fix extern error type

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.13.3...v0.13.4

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Published by AroneyS 6 months ago

binchicken - v0.13.3

Fixes to binchicken build env variable setup.

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.13.2...v0.13.3

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Published by AroneyS 6 months ago

binchicken - v0.13.2

What's Changed

Better error handling for snakemake rules, should print the log of the erroring rule and not allow snakemake to delete them with retries (https://github.com/AroneyS/binchicken/pull/186)
Fix build without args (https://github.com/AroneyS/binchicken/pull/187)
Minor bug fixes

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.13.1...v0.13.2

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Published by AroneyS 6 months ago

binchicken - v0.13.1

What's Changed

build: set env variables in the main pixi env too
Update Aviary to fix preparebinningfiles_split bug

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.13.0...v0.13.1

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Published by AroneyS 6 months ago

binchicken - v0.13.0

What's Changed

Switch to pixi for handling dependency environments (https://github.com/AroneyS/binchicken/pull/175)
Split preclustering into chunks to improve memory usage (https://github.com/AroneyS/binchicken/pull/176)
Better retries for cluster graph to further reduce combinatorial explosions with subsequent attempts (https://github.com/AroneyS/binchicken/pull/179)
Handle Bin Chicken vs SingleM sample naming properly (https://github.com/AroneyS/binchicken/pull/181)

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.12.11...v0.13.0

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Published by AroneyS 7 months ago

binchicken - v1.0.0beta1

Testing pixi install through conda for upcoming v1.0.0.

What's Changed

split preclustering into chunks by @AroneyS in https://github.com/AroneyS/binchicken/pull/176
Switch to pixi by @AroneyS in https://github.com/AroneyS/binchicken/pull/175

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.12.11...v1.0.0beta1

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Published by AroneyS 7 months ago

binchicken - v0.12.11

revert to secret pypi

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Published by AroneyS 10 months ago

binchicken - v0.12.10

pypi?

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Published by AroneyS 10 months ago

binchicken - v0.12.9

another pypi release....

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Published by AroneyS 10 months ago

binchicken - v0.12.8

Pypi release

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Published by AroneyS 10 months ago

binchicken - v0.12.7

Primarily changes to improve performance and memory usage with >750,000 samples.

What's Changed

Add conda for countbpreads by @AroneyS in https://github.com/AroneyS/binchicken/pull/156
Add sra argument to coassemble by @AroneyS in https://github.com/AroneyS/binchicken/pull/157
Implement anchor_samples argument by @AroneyS in https://github.com/AroneyS/binchicken/pull/160
Add extra binners arg by @AroneyS in https://github.com/AroneyS/binchicken/pull/161
Include qc folder in update by @AroneyS in https://github.com/AroneyS/binchicken/pull/162
Improve sketch samples by @AroneyS in https://github.com/AroneyS/binchicken/pull/163
Add aviary-snakemake-profile argument by @AroneyS in https://github.com/AroneyS/binchicken/pull/167
Use list arg for singlem summarise by @AroneyS in https://github.com/AroneyS/binchicken/pull/170
Target elusive speed up by @AroneyS in https://github.com/AroneyS/binchicken/pull/168
Account for huge inputs by @AroneyS in https://github.com/AroneyS/binchicken/pull/171
Switch to shell scripts by @AroneyS in https://github.com/AroneyS/binchicken/pull/173
Add skip-binners and request-gpu aviary recover args by @AroneyS in https://github.com/AroneyS/binchicken/pull/174

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.12.6...v0.12.7

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Published by AroneyS 10 months ago

binchicken - v0.12.6

What's Changed

Change default appraise by @AroneyS in https://github.com/AroneyS/binchicken/pull/142
Allow normal regex for taxa-of-interest argument by @AroneyS in https://github.com/AroneyS/binchicken/pull/143
Update README.md by @wwood in https://github.com/AroneyS/binchicken/pull/144
Fix enumeration of all combinations before filtering to top 100 by @AroneyS in https://github.com/AroneyS/binchicken/pull/145
Fix suffixes not being removed in preclusters by @AroneyS in https://github.com/AroneyS/binchicken/pull/146
Allow provided assemblies by @AroneyS in https://github.com/AroneyS/binchicken/pull/147
Change prior header to be consistent for single and update by @AroneyS in https://github.com/AroneyS/binchicken/pull/148
Add precluster distances argument by @AroneyS in https://github.com/AroneyS/binchicken/pull/150
Run no genomes in lazy mode by @AroneyS in https://github.com/AroneyS/binchicken/pull/151
Update docs by @AroneyS in https://github.com/AroneyS/binchicken/pull/152
Bump aviary to v0.10.0 by @AroneyS in https://github.com/AroneyS/binchicken/pull/153

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.12.5...v0.12.6

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Published by AroneyS over 1 year ago

binchicken - v0.12.5

What's Changed

Add separate subcommand for single-assembly by @AroneyS in https://github.com/AroneyS/binchicken/pull/140

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.12.4...v0.12.5

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Published by AroneyS over 1 year ago

binchicken - v0.12.4

New release to match docker release

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.12.3...v0.12.4

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Published by AroneyS over 1 year ago

binchicken - v0.12.2

What's Changed

Fix abundance weighting by @AroneyS in https://github.com/AroneyS/binchicken/pull/132
Add coassemblies list arg to update by @AroneyS in https://github.com/AroneyS/binchicken/pull/134
Update polars to v1.x by @AroneyS in https://github.com/AroneyS/binchicken/pull/133
Fix update on output without genomes by @AroneyS in https://github.com/AroneyS/binchicken/pull/138
Download databases by @AroneyS in https://github.com/AroneyS/binchicken/pull/121

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.12.1...v0.12.2

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Published by AroneyS over 1 year ago

binchicken - v0.12.1

Fix pip packaging

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.12.0...v0.12.1

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Published by AroneyS over 1 year ago

binchicken - v0.12.0

Major changes

Kmer preclustering allows Bin Chicken to scale beyond 250k samples
Abundance weighting biases coassembly selection to those estimated to recover highly abundant but unrecovered lineages

What's Changed

Kmer preselection by @AroneyS in https://github.com/AroneyS/binchicken/pull/113
Restrict sra downloading by @AroneyS in https://github.com/AroneyS/binchicken/pull/124
Add download-limit arg by @AroneyS in https://github.com/AroneyS/binchicken/pull/125
Remove filtering from query processing by @AroneyS in https://github.com/AroneyS/binchicken/pull/127
Switch to sourmash concatenate by @AroneyS in https://github.com/AroneyS/binchicken/pull/128
Abundance weighting by @AroneyS in https://github.com/AroneyS/binchicken/pull/129
Add abundance weighting samples arg by @AroneyS in https://github.com/AroneyS/binchicken/pull/130
Update aviary_commands to match smk rule by @AroneyS in https://github.com/AroneyS/binchicken/pull/131

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.11.0...v0.12.0

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Published by AroneyS over 1 year ago

binchicken - v0.11.0

What's Changed

fix binchicken suffix trimming by @AroneyS in https://github.com/AroneyS/binchicken/pull/118
Fix nontargets evaluation by @AroneyS in https://github.com/AroneyS/binchicken/pull/119
Error updates by @AroneyS in https://github.com/AroneyS/binchicken/pull/120
Update SingleM to v0.18 by @AroneyS in https://github.com/AroneyS/binchicken/pull/123
Remove GTDBtk from Aviary fast by @AroneyS in https://github.com/AroneyS/binchicken/pull/122

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.10.5...v0.11.0

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Published by AroneyS over 1 year ago

binchicken - v0.10.5

What's Changed

Update dependencies by @AroneyS in https://github.com/AroneyS/binchicken/pull/111
Fix filter bam naming bug by @AroneyS in https://github.com/AroneyS/binchicken/pull/112 (Thanks Andy Leu)
Fix tmpdir by @AroneyS in https://github.com/AroneyS/binchicken/pull/114
Harden evaluate by @AroneyS in https://github.com/AroneyS/binchicken/pull/116
Add coverage to evaluate by @AroneyS in https://github.com/AroneyS/binchicken/pull/117
Update Aviary by @AroneyS in https://github.com/AroneyS/binchicken/pull/115

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.10.4...v0.10.5

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Published by AroneyS almost 2 years ago

binchicken - v0.10.4

What's Changed

Add doctave-based docs by @AroneyS in https://github.com/AroneyS/binchicken/pull/101
bin: Improve help msgs. by @wwood in https://github.com/AroneyS/binchicken/pull/102
Improve snakemake retry behaviour by @AroneyS in https://github.com/AroneyS/binchicken/pull/105
Reduce update required inputs by @AroneyS in https://github.com/AroneyS/binchicken/pull/106
fix COASSEMBLY_SAMPLES causing lengths to get out of sync by @AroneyS in https://github.com/AroneyS/binchicken/pull/107
Improve Aviary running by @AroneyS in https://github.com/AroneyS/binchicken/pull/108
Notify if any sample skipped by @AroneyS in https://github.com/AroneyS/binchicken/pull/109
Update improvements by @AroneyS in https://github.com/AroneyS/binchicken/pull/110

New Contributors

@wwood made their first contribution in https://github.com/AroneyS/binchicken/pull/102

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.10.3...v0.10.4

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Published by AroneyS almost 2 years ago

binchicken - v0.10.3

What's Changed

Add links and citation by @AroneyS in https://github.com/AroneyS/binchicken/pull/100

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.10.2...v0.10.3

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Published by AroneyS about 2 years ago

binchicken - v0.10.2

Fix pypi upload

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Published by AroneyS about 2 years ago

binchicken - v0.10.1

New release for Zenodo
Increase memory for rules with retries

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.10.0...v0.10.1

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Published by AroneyS about 2 years ago

binchicken - v0.10.0

What's Changed

Quality of life improvements by @AroneyS in https://github.com/AroneyS/binchicken/pull/86
- Rename --aviary-[gtdbtk, checkm2]-dir args to --aviary-[gtdbtk, checkm2]-db
- Add database env variables to ibis build (SingleM, CheckM2, GTDBtk)
- Minimise standard workflow arguments
- Removed --no-genomes argument and made that the default
- Set max size to 50Gbp unless single-assembly
Add Aviary build to Ibis build by @AroneyS in https://github.com/AroneyS/binchicken/pull/89
Snakefile improvements by @AroneyS in https://github.com/AroneyS/binchicken/pull/93
Update dependencies by @AroneyS in https://github.com/AroneyS/binchicken/pull/94
Improve genome loading by @AroneyS in https://github.com/AroneyS/binchicken/pull/95
Change name to binchicken by @AroneyS in https://github.com/AroneyS/binchicken/pull/96

Breaking changes

--coassemble-output now refers to --output dir from coassemble command instead of referring to the coassemble subfolder within that output dir
Rename --aviary-[gtdbtk, checkm2]-dir args to --aviary-[gtdbtk, checkm2]-db
Removed --no-genomes argument and made that the default
Set max size to 50Gbp unless single-assembly

Full Changelog: https://github.com/AroneyS/binchicken/compare/v0.9.6...v0.10.0

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Published by AroneyS about 2 years ago

binchicken - v0.9.6

What's Changed

Add input to restrict coassembly samples by @AroneyS in https://github.com/AroneyS/ibis/pull/71
Add SingleM metapackage env var by @AroneyS in https://github.com/AroneyS/ibis/pull/75
Update Aviary env by @AroneyS in https://github.com/AroneyS/ibis/pull/78
Fix using max recovery samples with single assembly by @AroneyS in https://github.com/AroneyS/ibis/pull/79

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.9.5...v0.9.6

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Published by AroneyS over 2 years ago

binchicken - v0.9.5

What's Changed

Fix split sra downloads by @AroneyS in https://github.com/AroneyS/ibis/pull/59
Prevent aviary recover output deletion by @AroneyS in https://github.com/AroneyS/ibis/pull/61
Update polars to v0.19 by @AroneyS in https://github.com/AroneyS/ibis/pull/63
Add more suffix options by @AroneyS in https://github.com/AroneyS/ibis/pull/64
Update SingleM by @AroneyS in https://github.com/AroneyS/ibis/pull/65
Skip single-ended on rerun by @AroneyS in https://github.com/AroneyS/ibis/pull/67
Fix QC by @AroneyS in https://github.com/AroneyS/ibis/pull/68
Update dependencies by @AroneyS in https://github.com/AroneyS/ibis/pull/70

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.9.4...v0.9.5

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Published by AroneyS over 2 years ago

binchicken - v0.9.4

What's Changed

Switch to cores arg for snakemake by @AroneyS in https://github.com/AroneyS/ibis/pull/48
Remove bbduk qc filtering by @AroneyS in https://github.com/AroneyS/ibis/pull/49
Remove use of -- before target rule/file by @AroneyS in https://github.com/AroneyS/ibis/pull/51
Restrict polars threads in main by @AroneyS in https://github.com/AroneyS/ibis/pull/53
Switch to Fastp QC by @AroneyS in https://github.com/AroneyS/ibis/pull/55
Separate read downloading by @AroneyS in https://github.com/AroneyS/ibis/pull/57

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.9.3...v0.9.4

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Published by AroneyS over 2 years ago

binchicken - v0.9.3

What's Changed

Deduplicate contig names in incoming genomes for unmapping by @AroneyS in https://github.com/AroneyS/ibis/pull/40
Add coassemble arg by @AroneyS in https://github.com/AroneyS/ibis/pull/42
Filter out samples not present in forward input by @AroneyS in https://github.com/AroneyS/ibis/pull/45
update kingfisher to v0.3.0 by @AroneyS in https://github.com/AroneyS/ibis/pull/46

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.9.2...v0.9.3

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Published by AroneyS over 2 years ago

binchicken - v0.9.2

What's Changed

Better snakemake cluster support by @AroneyS in https://github.com/AroneyS/ibis/pull/39

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.9.1...v0.9.2

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Published by AroneyS over 2 years ago

binchicken - v0.9.1

What's Changed

Fix _1 being used instead of .1 by @AroneyS in https://github.com/AroneyS/ibis/pull/38

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.9.0...v0.9.1

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Published by AroneyS over 2 years ago

binchicken - v0.9.0

What's Changed

Fix conda env versions by @AroneyS in https://github.com/AroneyS/ibis/pull/21
Switch to greedy algorithm by @AroneyS in https://github.com/AroneyS/ibis/pull/22
Add build subcommand by @AroneyS in https://github.com/AroneyS/ibis/pull/25
Fix target elusive memory issues by @AroneyS in https://github.com/AroneyS/ibis/pull/26
Separate single-assembly from no-genomes by @AroneyS in https://github.com/AroneyS/ibis/pull/27
Add new genomes input by @AroneyS in https://github.com/AroneyS/ibis/pull/28
Update evaluate by @AroneyS in https://github.com/AroneyS/ibis/pull/29
Improve iterate by @AroneyS in https://github.com/AroneyS/ibis/pull/30
Update polars to v0.18.11 by @AroneyS in https://github.com/AroneyS/ibis/pull/31
Fix cluster graph memory by @AroneyS in https://github.com/AroneyS/ibis/pull/32
Fix aviary commands by @AroneyS in https://github.com/AroneyS/ibis/pull/33
Update Aviary to v0.7.0 by @AroneyS in https://github.com/AroneyS/ibis/pull/34
Add --new-genome-singlem argument to iterate by @AroneyS in https://github.com/AroneyS/ibis/pull/35
SRA downloading improvements by @AroneyS in https://github.com/AroneyS/ibis/pull/36
Support snakemake cluster by @AroneyS in https://github.com/AroneyS/ibis/pull/37

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.8.0...v0.9.0

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Published by AroneyS over 2 years ago

binchicken - v0.8.0

What's Changed

Update unmap by @AroneyS in https://github.com/AroneyS/ibis/pull/18
- renamed update
- primarily for generating unmapped reads, running Aviary commands and/or downloading SRA reads
Check for interleaved SRA by @AroneyS in https://github.com/AroneyS/ibis/pull/19
- Account for interleaved and single-end reads from SRA (deinterleave and raise error, respectively)
Add aligned fraction unmapping by @AroneyS in https://github.com/AroneyS/ibis/pull/20
- Switch to using --min-read-percent-identity-pair and --min-read-aligned-percent-pair for CoverM unmapping
- Default to 99% for both arguments

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.7.2...v0.8.0

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Published by AroneyS almost 3 years ago

binchicken - v0.7.2

What's Changed

Add taxa of interest filtering to query_processing by @AroneyS in https://github.com/AroneyS/ibis/pull/17

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.7.1...v0.7.2

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Published by AroneyS almost 3 years ago

binchicken - v0.7.1

Fix pypi uploading

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.7.0...v0.7.1

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Published by AroneyS almost 3 years ago

binchicken - v0.7.0

What's Changed

Remove S3.18.EIF2alpha sequences by @AroneyS in https://github.com/AroneyS/ibis/pull/15
Account for nontarget unbinned sequences in evaluate script by @AroneyS in https://github.com/AroneyS/ibis/pull/16
update unmapping max identity default to 99%

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.6.0...v0.7.0

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Published by AroneyS almost 3 years ago

binchicken - v0.6.0

What's Changed

Add argument to select specific coassemblies to unmap by @AroneyS in https://github.com/AroneyS/ibis/pull/11
Switch from pandas to polars (much faster!) by @AroneyS in https://github.com/AroneyS/ibis/pull/12
Add no-genomes argument for coassembly from scratch by @AroneyS in https://github.com/AroneyS/ibis/pull/14

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.5.1...v0.6.0

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Published by AroneyS almost 3 years ago

binchicken - v0.5.1

What's Changed

Add SRA-specific commands by @AroneyS in https://github.com/AroneyS/ibis/pull/3
- Includes --sra argument to download SRA readsets
- Includes --run-aviary to attempt to run aviary locally
- Unable to implement properly due to https://github.com/snakemake/snakemake/issues/1998, potentially fixed with https://github.com/snakemake/snakemake/pull/1708. Aviary must be given as path to prebuilt conda env due to database setup requirements.

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.5.0...v0.5.1

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Published by AroneyS about 3 years ago

binchicken - v0.5.0

What's Changed

Improve unmapping by @AroneyS in https://github.com/AroneyS/ibis/pull/8
account for all clusters being filtered out by @AroneyS in https://github.com/AroneyS/ibis/pull/9
Fix evaluate errors with multiple coassemblies by @AroneyS in https://github.com/AroneyS/ibis/pull/7
Change name to Ibis by @AroneyS in https://github.com/AroneyS/ibis/pull/10

Full Changelog: https://github.com/AroneyS/ibis/compare/v0.4.8...v0.5.0

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Published by AroneyS about 3 years ago

binchicken - v0.4.8

What's Changed

Account for queried sequences returning no hits by @AroneyS in https://github.com/AroneyS/cockatoo/pull/4
Create iterate subcommand by @AroneyS in https://github.com/AroneyS/cockatoo/pull/5
Evaluate improvements by @AroneyS in https://github.com/AroneyS/cockatoo/pull/6

Full Changelog: https://github.com/AroneyS/cockatoo/compare/v0.4.7...v0.4.8

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Published by AroneyS about 3 years ago

binchicken - v0.4.7

Restrict SingleM in parallel by assuming each takes 8 threads (SingleM does not honor threads contract)
Update SingleM to v1.0.0beta2
Add -t CPUS argument to Aviary commands to enable rules to use more than 8 threads (default)

Full Changelog: https://github.com/AroneyS/cockatoo/compare/v0.4.6...v0.4.7

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Published by AroneyS about 3 years ago