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

#151 - How to run create_aviary_webpage.py?

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

#150 - Silent errors in aviary diversity

Issue - State: closed - Opened by Ge0rges over 1 year ago - 2 comments

#149 - Error in prepare_binning_files

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

#148 - Aviary recover missing input files for prepapre_binning_files

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

#147 - Support for MetaBinner

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

#146 - Potential bug in medaka polishing call

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

#145 - v0.8.1 into main

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

#144 - Fix arg parsing issue

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

#143 - Undefined variable error in 0.8.0

Issue - State: closed - Opened by Ge0rges over 1 year ago - 2 comments

#142 - Merge Dev into Main

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

#141 - bump to v0.8.0

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

#140 - Missing raw_mapped_ref.bai file when using --reference-filter flag

Issue - State: closed - Opened by Ge0rges over 1 year ago - 7 comments

#139 - fix: link reads was not properly account for coassemble flag

Pull Request - State: closed - Opened by rhysnewell over 1 year ago - 8 comments

#138 - Run only QC?

Issue - State: closed - Opened by Ge0rges over 1 year ago - 10 comments

#137 - Error with SPAdes

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

#136 - Conda can't create seqtk environment due to pigs requirement

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

#135 - Decontamination in QC?

Issue - State: closed - Opened by Ge0rges over 1 year ago - 3 comments

#134 - `--coassemble` ambiguity

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

#133 - Benchmark on CAMI2?

Issue - State: closed - Opened by Ge0rges over 1 year ago - 2 comments

#132 - Make long read qc temp

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

#131 - Remove upper snakemake bound

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

#130 - Repeat experiment

Issue - State: closed - Opened by MoroNesterov over 1 year ago - 1 comment

#129 - Better snakemake cluster submission support

Pull Request - State: closed - Opened by AroneyS over 1 year ago - 13 comments

#128 - Catchup dev to main

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

#127 - fix empty bin_info.tsv with --skip-abundances

Pull Request - State: closed - Opened by AroneyS over 1 year ago - 5 comments

#126 - v0.7.2

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

#125 - bump version

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

#124 - V0.7.2

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

#123 - Implement skip abundances arg

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

#122 - IndexError: list index out of range

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

#121 - refinery: only copy actual bins

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

#120 - IsADirectoryError in rosella_refine.py

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

#119 - v0.7.1

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

#118 - fixed combine assembly script, fixes #117

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

#117 - AttributeError: 'InputFiles' object has no attribute 'flye_fasta'

Issue - State: closed - Opened by sternp over 1 year ago - 1 comment

#116 - update deploy docs

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

#115 - add: homebrew setup in actions

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

#114 - Update docs changes so they also occur on dev branch

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

#113 - update: docs workflow

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

#112 - update: documentation branch from master to main

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

#111 - Merge v0.7.0 to main

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

#110 - update: v0.7.0

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

#109 - Citations update

Pull Request - State: closed - Opened by wwood over 1 year ago - 8 comments

#108 - Concoct error

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

#107 - fix: removal of instances of shell=True

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

#106 - Incorporating SemiBin2?

Issue - State: closed - Opened by julianzaugg over 1 year ago - 2 comments

#105 - Fix checkm subprocess

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

#104 - Update to semibin2

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

#103 - Add refinery max iterations arg

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

#102 - Catch dev up to main

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

#101 - Rework skip-binners

Pull Request - State: closed - Opened by AroneyS over 1 year ago - 5 comments

#100 - Fix Vamb-jgi-filter memory issues

Pull Request - State: closed - Opened by AroneyS over 1 year ago - 11 comments

#99 - vamb_jgi_filter segmentation faults

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

#98 - update version to v0.6.0 on main

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

#97 - Merge Medaka into Dev

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

#96 - Merge Dev into Main

Pull Request - State: closed - Opened by rhysnewell over 1 year ago - 5 comments

#95 - Merge main into dev

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

#92 - Error when running recover pipeline

Issue - State: closed - Opened by 0x1d4e about 2 years ago - 13 comments

#91 - Add medaka polishing

Pull Request - State: closed - Opened by rhysnewell about 2 years ago - 1 comment

#90 - Conda install fails with "UnsatisfiableError"

Issue - State: closed - Opened by KatharinaHoff about 2 years ago - 3 comments

#89 - Nanopore should be corrected by medaka

Issue - State: closed - Opened by wwood about 2 years ago - 1 comment

#88 - Fixes #87, argparse input long-read-type as string not list

Pull Request - State: closed - Opened by rhysnewell about 2 years ago

#86 - Container

Issue - State: open - Opened by vmurigneu about 2 years ago - 2 comments
Labels: good first issue

#85 - Merge Dev, close #84

Pull Request - State: closed - Opened by rhysnewell about 2 years ago

#84 - Rosella bins not used due to command mis-spelling

Issue - State: closed - Opened by AroneyS about 2 years ago - 3 comments

#83 - fix: closes #82 fix typo on rerun_triggers

Pull Request - State: closed - Opened by rhysnewell about 2 years ago

#82 - KeyError: 'rerun_trigger' in version 0.5.5

Issue - State: closed - Opened by sternp about 2 years ago - 1 comment

#81 - concoct hanging / --skip-binners concoct not working aviary 0.5.4

Issue - State: closed - Opened by gbouras13 about 2 years ago - 5 comments

#80 - Fix paired end reads mismatching

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

#79 - MultiQC in Aviary cluster errors on some samples

Issue - State: closed - Opened by sternp over 2 years ago - 2 comments

#78 - template_config.yaml

Issue - State: closed - Opened by yikiii over 2 years ago - 4 comments

#77 - Configuration of aviary with hpc scheduler

Issue - State: closed - Opened by Rridley7 over 2 years ago - 8 comments

#76 - Lack of --meta?

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

#75 - test: Add short read recover.

Pull Request - State: closed - Opened by wwood over 2 years ago - 7 comments

#74 - Minimal testing

Pull Request - State: closed - Opened by wwood over 2 years ago

#73 - EmptyDataError in Aviary recover with long and short reads

Issue - State: closed - Opened by AroneyS over 2 years ago - 15 comments

#72 - Type error when using Aviary cluster

Issue - State: closed - Opened by sternp over 2 years ago - 3 comments

#71 - TypeError in Aviary assemble with multiple short-reads

Issue - State: closed - Opened by AroneyS over 2 years ago - 18 comments

#70 - configure: Namespace error

Issue - State: closed - Opened by wwood over 2 years ago - 1 comment

#68 - README: Requirements section needed?

Issue - State: closed - Opened by wwood over 2 years ago

#67 - Multi-Sample Functionality

Issue - State: closed - Opened by gbouras13 over 2 years ago - 5 comments

#66 - Exporting environmental CHECKM2DB does not work?

Issue - State: closed - Opened by julianzaugg over 2 years ago - 5 comments

#64 - License confusion

Issue - State: closed - Opened by cbrueffer over 2 years ago - 1 comment

#63 - Error when run aviary: ModuleNotFoundError: No module named 'aviary.config'

Issue - State: closed - Opened by kevinzhongxu over 2 years ago - 9 comments

#62 - singlem

Issue - State: closed - Opened by gbouras13 over 2 years ago - 3 comments

#61 - finalize_stats and get_abundances does not seem to be in the DAG

Issue - State: closed - Opened by gbouras13 over 2 years ago - 1 comment

#60 - assembly folder name can be misleading

Issue - State: closed - Opened by wwood over 2 years ago

#59 - Potential duplication of contigs occuring [Probably false alarm]

Issue - State: closed - Opened by rhysnewell over 2 years ago - 2 comments

#58 - lorikeet error

Issue - State: closed - Opened by gbouras13 over 2 years ago - 5 comments

#57 - Update run_lorikeet.py to fix typo

Pull Request - State: closed - Opened by gbouras13 over 2 years ago - 1 comment

#56 - lorikeet.smk snakemake typo

Issue - State: closed - Opened by gbouras13 over 2 years ago - 1 comment

#55 - README update

Issue - State: closed - Opened by wwood over 2 years ago - 1 comment

#54 - checkm.out strange 0 completeness and marker genes for large bins

Issue - State: closed - Opened by gbouras13 over 2 years ago - 11 comments

#53 - Lorikeet Installation Fails 0.7.1

Issue - State: closed - Opened by gbouras13 over 2 years ago - 3 comments

#52 - Offline Installation

Issue - State: closed - Opened by gbouras13 over 2 years ago - 4 comments