Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / rhysnewell/aviary issues and pull requests

#248 - Pep 625 fix

Pull Request - State: open - Opened by rhysnewell 9 days ago

#247 - Update snakemake

Pull Request - State: open - Opened by AroneyS 15 days ago - 2 comments

#247 - Update snakemake

Pull Request - State: open - Opened by AroneyS 15 days ago - 2 comments

#246 - Need to update PR to fix new tests

Pull Request - State: closed - Opened by AroneyS 15 days ago

#245 - VAMB error due to new version

Issue - State: open - Opened by AroneyS 15 days ago

#245 - VAMB error due to new version

Issue - State: open - Opened by AroneyS 15 days ago

#244 - Add TaxVAMB

Pull Request - State: closed - Opened by AroneyS 17 days ago - 1 comment

#243 - MissingOutputException in rule singlem_appraise

Issue - State: open - Opened by Anna-MarieSeelen 19 days ago - 1 comment

#242 - citation: Add preferred-citation, change title.

Pull Request - State: closed - Opened by wwood about 1 month ago - 1 comment

#241 - chore: Update CITATION.cff to 0.10.0

Pull Request - State: closed - Opened by wwood about 1 month ago - 4 comments

#240 - Readd pplacer threads

Pull Request - State: closed - Opened by AroneyS about 2 months ago

#239 - Use config as env source

Pull Request - State: closed - Opened by AroneyS about 2 months ago - 2 comments

#238 - recover: When file inputs are wrong, error is not graceful

Issue - State: open - Opened by wwood about 2 months ago

#237 - errors downloading dbs

Issue - State: open - Opened by microbemarsh 2 months ago - 9 comments

#236 - KeyError for `SINGLEM_METAPACKAGE_PATH`

Issue - State: open - Opened by AroneyS 2 months ago

#235 - Switch to semibin2 interface

Pull Request - State: closed - Opened by AroneyS 2 months ago - 1 comment

#234 - Add COMEbin as another default binner

Pull Request - State: open - Opened by AroneyS 2 months ago - 4 comments

#233 - Switch to using Semibin2 interface

Issue - State: open - Opened by AroneyS 2 months ago

#232 - change pplacer threads to 1 in processor.py

Pull Request - State: closed - Opened by Anna-MarieSeelen 2 months ago - 3 comments

#231 - Cannot allocate memory GTDB-Tk

Issue - State: open - Opened by Anna-MarieSeelen 2 months ago - 2 comments

#230 - Dev

Pull Request - State: closed - Opened by rhysnewell 2 months ago

#229 - .gitignore: Add further aviary outputs.

Pull Request - State: closed - Opened by wwood 2 months ago

#228 - metaMDBG

Pull Request - State: open - Opened by wwood 2 months ago

#227 - Fix vamb being excluded from dastool

Pull Request - State: closed - Opened by AroneyS 3 months ago

#226 - Switch memory multiplier to 1000

Pull Request - State: closed - Opened by AroneyS 3 months ago - 4 comments

#224 - Increase base vamb runtime to 48h

Pull Request - State: closed - Opened by AroneyS 3 months ago

#223 - assemble/recover: Require users to specify coassembly or not.

Pull Request - State: closed - Opened by wwood 3 months ago - 8 comments

#222 - aviary: Update --build help message.

Pull Request - State: closed - Opened by wwood 3 months ago - 1 comment

#221 - actions: test-aviary: Attempt fix.

Pull Request - State: closed - Opened by wwood 3 months ago - 1 comment

#220 - config.yaml: Remove this extraneous file.

Pull Request - State: closed - Opened by wwood 3 months ago

#219 - --no-coassembly flag?

Issue - State: closed - Opened by wwood 3 months ago - 1 comment

#218 - recommended way to build conda envs

Issue - State: closed - Opened by wwood 3 months ago - 2 comments

#217 - Bio module not found in script

Issue - State: open - Opened by wwood 3 months ago - 1 comment

#216 - spades: Update to 4.

Pull Request - State: closed - Opened by wwood 3 months ago - 4 comments

#215 - Add pyproject.toml.

Pull Request - State: closed - Opened by wwood 3 months ago - 1 comment

#214 - spades issues due to setuptools not specified in the env file

Issue - State: closed - Opened by michoug 4 months ago - 2 comments

#213 - Merge dev to main

Pull Request - State: closed - Opened by rhysnewell 5 months ago

#212 - Fix checkm2 env

Pull Request - State: closed - Opened by AroneyS 5 months ago

#211 - Contig size parameter not working properly

Issue - State: open - Opened by dylancronin 6 months ago - 1 comment

#210 - Error with Vamb

Issue - State: closed - Opened by aljazdzy 7 months ago - 1 comment

#209 - conda package doesn't have pplacer_threads option?

Issue - State: open - Opened by CJREID 7 months ago - 2 comments

#208 - refine_metabat2 running out of memory

Issue - State: open - Opened by CJREID 8 months ago - 8 comments

#207 - Update annotation.smkwith new GTDB DB URL

Pull Request - State: closed - Opened by JamesRH 8 months ago - 2 comments

#206 - Hybrid spades assembly question

Issue - State: open - Opened by aleuQUT 8 months ago - 2 comments

#204 - --coassemble flag inquiry

Issue - State: open - Opened by lcamVz 9 months ago

#203 - merging v0.9.1

Pull Request - State: closed - Opened by rhysnewell 9 months ago - 2 comments

#202 - fix: batch checks read type correctly

Pull Request - State: closed - Opened by rhysnewell 9 months ago

#201 - convert rule spades_assembly to a python script

Pull Request - State: closed - Opened by YibiChen 10 months ago - 12 comments

#200 - fix tmpdir being set from base command

Pull Request - State: closed - Opened by AroneyS 10 months ago - 22 comments

#199 - fix: batch submission now does not require user to write to script first

Pull Request - State: closed - Opened by rhysnewell 10 months ago - 3 comments

#198 - How to run aviary with a batch file

Issue - State: closed - Opened by s-junguy 10 months ago - 5 comments

#197 - chore: Update CITATION.cff

Pull Request - State: closed - Opened by rhysnewell 11 months ago

#196 - release v0.9.0

Pull Request - State: closed - Opened by rhysnewell 11 months ago

#195 - Complete error

Issue - State: closed - Opened by Josue-B-Navarrete 11 months ago - 12 comments

#194 - CheckM Rosella file not found

Issue - State: open - Opened by sternp about 1 year ago - 3 comments

#193 - Error with CheckM2 and Rosella

Issue - State: closed - Opened by ronjasan about 1 year ago - 9 comments

#192 - Adding binning-only flag, simplify recipes

Pull Request - State: closed - Opened by rhysnewell about 1 year ago - 20 comments

#191 - Mamba error creating Rosella env

Issue - State: closed - Opened by AroneyS about 1 year ago - 11 comments

#189 - Loosen same-group permissions for folders and logs

Pull Request - State: closed - Opened by AroneyS about 1 year ago - 1 comment

#188 - Snakemake doesn't respect umask value

Issue - State: closed - Opened by AroneyS about 1 year ago - 1 comment

#187 - das_tool: Use script not shell.

Pull Request - State: closed - Opened by wwood about 1 year ago - 1 comment

#186 - skipping metabat

Issue - State: closed - Opened by wwood about 1 year ago - 2 comments

#185 - binning only

Issue - State: closed - Opened by wwood about 1 year ago - 1 comment

#184 - Doco updates

Pull Request - State: closed - Opened by wwood about 1 year ago

#183 - Running aviary directly from a git checkout

Issue - State: closed - Opened by wwood about 1 year ago - 2 comments

#182 - qc not generating a readset

Issue - State: closed - Opened by wwood about 1 year ago - 1 comment

#181 - independent singlem runs

Issue - State: closed - Opened by wwood about 1 year ago

#180 - --use-conda versus --conda-frontend

Issue - State: closed - Opened by blindner6 about 1 year ago - 1 comment

#179 - threading issues and rosella version

Pull Request - State: closed - Opened by rhysnewell about 1 year ago - 2 comments

#178 - singlem threads and 16

Issue - State: closed - Opened by wwood about 1 year ago - 2 comments

#177 - singlem: Update to 0.16.0.

Pull Request - State: closed - Opened by wwood about 1 year ago - 3 comments

#176 - megahit: Specify -m in bytes.

Pull Request - State: closed - Opened by wwood about 1 year ago

#175 - cff-update: Update to v0.8.3.

Pull Request - State: closed - Opened by wwood about 1 year ago - 1 comment

#174 - threads

Issue - State: closed - Opened by wwood about 1 year ago - 7 comments

#173 - Add SingleM metapackage downloading

Pull Request - State: closed - Opened by AroneyS about 1 year ago - 2 comments

#172 - v0.8.3 release to main

Pull Request - State: closed - Opened by rhysnewell about 1 year ago

#171 - Set pplacer threads

Pull Request - State: closed - Opened by AroneyS about 1 year ago - 1 comment

#169 - SyntaxWarning

Issue - State: closed - Opened by AroneyS about 1 year ago - 1 comment

#168 - Update rosella to v0.5.0

Pull Request - State: closed - Opened by rhysnewell about 1 year ago - 45 comments

#167 - attempt to fix #166 by interleaving reads correctly

Pull Request - State: closed - Opened by rhysnewell over 1 year ago - 6 comments

#166 - Skip QC produces concatenated (not interleaved) short-reads

Issue - State: closed - Opened by AroneyS over 1 year ago - 9 comments

#165 - error using aviary configure

Issue - State: closed - Opened by rikander over 1 year ago - 9 comments

#164 - Error using -r flag

Issue - State: closed - Opened by Ge0rges over 1 year ago - 4 comments

#163 - SPAdes not running during hybrid assembly mode

Issue - State: closed - Opened by hisatakeishida over 1 year ago - 18 comments

#162 - citations: Improve them.

Pull Request - State: closed - Opened by wwood over 1 year ago - 4 comments

#161 - update main to v0.8.2

Pull Request - State: closed - Opened by rhysnewell over 1 year ago

#160 - v0.8.2

Pull Request - State: closed - Opened by rhysnewell over 1 year ago

#159 - singlem: Restrict to 0.13.2. Fixes #157.

Pull Request - State: closed - Opened by wwood over 1 year ago - 1 comment

#158 - FileNotFoundError in rule checkm_das_tool

Issue - State: closed - Opened by s-junguy over 1 year ago - 6 comments

#157 - singlem_appraise error

Issue - State: closed - Opened by microbemarsh over 1 year ago - 8 comments

#156 - Singlem update

Pull Request - State: closed - Opened by wwood over 1 year ago - 2 comments

#155 - Fix short read coassemble qc

Pull Request - State: closed - Opened by AroneyS over 1 year ago - 1 comment

#154 - Add fastp and update docs

Pull Request - State: closed - Opened by rhysnewell over 1 year ago

#153 - Update resources

Pull Request - State: closed - Opened by AroneyS over 1 year ago - 1 comment

#152 - Error in singlem log

Issue - State: closed - Opened by Ge0rges over 1 year ago - 5 comments

#151 - How to run create_aviary_webpage.py?

Issue - State: closed - Opened by Ge0rges over 1 year ago - 4 comments