Ecosyste.ms: Issues

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

GitHub / czbiohub-sf/MIDAS2 issues and pull requests

#138 - Errors when download the MIDASdb

Issue - State: open - Opened by yejunbin 6 months ago - 2 comments

#137 - Query regarding specificity of the tool

Issue - State: closed - Opened by sahilrishav2 6 months ago - 16 comments

#136 - midasv3 chunk size error with midas2 database init

Issue - State: closed - Opened by uel3 7 months ago - 2 comments

#135 - Support for bioconda/singularity/nextflow

Issue - State: open - Opened by uel3 8 months ago - 1 comment

#134 - midas version3 rc3 minor updates

Pull Request - State: closed - Opened by zhaoc1 8 months ago

#132 - 2024-03-05-v3rc3

Pull Request - State: closed - Opened by zhaoc1 9 months ago

#131 - 2024-03-04 v3rc2

Pull Request - State: closed - Opened by zhaoc1 9 months ago

#130 - midas version 3 rc 1

Pull Request - State: closed - Opened by zhaoc1 9 months ago

#129 - Error in building a customised database

Issue - State: closed - Opened by sahilrishav2 9 months ago - 4 comments

#127 - Feature request: Change how gene depth is estimated

Issue - State: closed - Opened by bsmith89 10 months ago - 4 comments

#126 - error in merge snps

Issue - State: closed - Opened by sophiejwalton 11 months ago - 3 comments

#125 - Update funannnot_parser

Pull Request - State: closed - Opened by zhaoc1 12 months ago

#124 - MIDAS2 v1.1.1 major updates

Pull Request - State: closed - Opened by zhaoc1 about 1 year ago

#122 - midas2 v1.0.9

Issue - State: closed - Opened by qinghong2019 about 1 year ago - 5 comments

#121 - Install from source needs additional channel

Issue - State: closed - Opened by mtisza1 about 1 year ago - 3 comments

#120 - How to keep the alignment?

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

#119 - v1.1.0

Pull Request - State: closed - Opened by zhaoc1 about 1 year ago

#118 - 2023 08 31 py3.9

Pull Request - State: closed - Opened by zhaoc1 about 1 year ago

#117 - scratch dir related

Pull Request - State: closed - Opened by zhaoc1 about 1 year ago

#116 - Update codes related to scratch dir

Pull Request - State: closed - Opened by zhaoc1 about 1 year ago

#115 - 2023 07 27/build midasdb

Pull Request - State: closed - Opened by zhaoc1 about 1 year ago

#114 - add bash script for recluster centroids

Pull Request - State: closed - Opened by zhaoc1 over 1 year ago

#113 - add import_genome subcommand

Pull Request - State: closed - Opened by zhaoc1 over 1 year ago

#112 - UHGG database download error

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

#111 - Add pan-genomes contigs length

Pull Request - State: closed - Opened by zhaoc1 over 1 year ago

#110 - add scratch dir option for HPC compute

Pull Request - State: closed - Opened by zhaoc1 over 1 year ago

#109 - 2023 06 23 recluster

Pull Request - State: closed - Opened by zhaoc1 over 1 year ago

#108 - merge_snps

Issue - State: closed - Opened by luoqingqing777 over 1 year ago - 2 comments

#106 - bwa-meme

Issue - State: closed - Opened by nick-youngblut about 2 years ago - 8 comments

#105 - Update species_module.rst

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

#104 - Use bining data as ref-genome

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

#103 - merge_snp issue still exist

Issue - State: closed - Opened by BaylorLyu about 2 years ago - 9 comments

#102 - how to build ughh database?

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

#101 - newdb related

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#100 - Update glossary.rst

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#99 - 2022 06 16/docs patch

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#98 - Update glossary.rst

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#97 - Update advanced_topics.rst

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#96 - Update output.rst

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#95 - Update output.rst

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#94 - Update download_midasdb.rst

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#93 - Update species_module.rst

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#92 - Update overview.rst

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#91 - Update quickstart.rst

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#90 - 2022 06 15/rename midas2

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago - 2 comments

#89 - add docs

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#88 - merge_snps error

Issue - State: closed - Opened by luoqingqing777 over 2 years ago - 8 comments

#87 - run_species error

Issue - State: closed - Opened by luoqingqing777 over 2 years ago

#86 - midasdb gtdb alive on the server

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#85 - midas2 database: does not list and download MIDAS DB

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

#84 - midasdb uhgg ready on ucsf server

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#83 - download failed

Issue - State: closed - Opened by snayfach over 2 years ago - 12 comments

#82 - add md5sum check

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#81 - Add feature of downloading files from HTTPS server instead of S3

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#80 - v0.9.5

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#79 - add ignore ambiguous sites

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#78 - v0.9.3 migrate s3 bucket

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#77 - add conda pkg recipe

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#76 - python packaging related

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#75 - update midas2.0 print

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#74 - Add database download/list command

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#73 - Rename repo from iggtools to MIDAS2.0

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#72 - 2022-03-02 chunyu/conda docker

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#71 - cleanup comments

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#70 - clean up comments

Pull Request - State: closed - Opened by zhaoc1 over 2 years ago

#69 - minor updates

Pull Request - State: closed - Opened by zhaoc1 almost 3 years ago

#68 - major updates from large sample amounts

Pull Request - State: closed - Opened by zhaoc1 almost 3 years ago

#67 - add analysis-ready option for bamfile

Pull Request - State: closed - Opened by zhaoc1 about 3 years ago

#66 - changes related to chunks and MIDASDB

Pull Request - State: closed - Opened by zhaoc1 about 3 years ago

#65 - pylint docker related updates

Pull Request - State: closed - Opened by zhaoc1 about 3 years ago

#64 - json int key into string

Pull Request - State: closed - Opened by zhaoc1 about 3 years ago

#63 - minor updates to the params

Pull Request - State: closed - Opened by zhaoc1 about 3 years ago

#62 - upgrade species flow from v0.33

Pull Request - State: closed - Opened by zhaoc1 about 3 years ago

#61 - update merge framework for v0.32

Pull Request - State: closed - Opened by zhaoc1 about 3 years ago

#60 - Chunyu/2021 08 31 species

Pull Request - State: closed - Opened by zhaoc1 about 3 years ago

#59 - Add --no-sign-request flag to 'aws s3 cp'

Pull Request - State: closed - Opened by bsmith89 about 3 years ago - 2 comments

#58 - Chunyu/2021 07 23 speed

Pull Request - State: closed - Opened by zhaoc1 about 3 years ago

#57 - minor updates for speed improvements

Pull Request - State: closed - Opened by zhaoc1 over 3 years ago

#56 - majors updates

Pull Request - State: closed - Opened by zhaoc1 over 3 years ago

#55 - major updates

Pull Request - State: closed - Opened by zhaoc1 over 3 years ago

#54 - update genes flow

Pull Request - State: closed - Opened by zhaoc1 over 3 years ago

#53 - Chunyu/20210310 genes

Pull Request - State: closed - Opened by zhaoc1 over 3 years ago

#52 - redesign chunks for the SNPs workflows

Pull Request - State: closed - Opened by zhaoc1 over 3 years ago

#51 - compare with MIDAS1.0 using midas_db_v1.2

Pull Request - State: closed - Opened by zhaoc1 almost 4 years ago

#50 - minor change to build_bowtie2_db

Pull Request - State: closed - Opened by zhaoc1 almost 4 years ago

#49 - update writing style in midas_merge_snps

Pull Request - State: closed - Opened by zhaoc1 almost 4 years ago

#48 - add performance prints to unit test

Pull Request - State: closed - Opened by zhaoc1 almost 4 years ago

#47 - exception handling in multiprocessing

Issue - State: closed - Opened by zhaoc1 almost 4 years ago - 1 comment
Labels: help wanted, technical debt

#46 - add gene annotation to midas_merge_snps

Pull Request - State: closed - Opened by zhaoc1 almost 4 years ago

#45 - [clean up] combine build_gene_features with annotate_genes

Issue - State: closed - Opened by zhaoc1 almost 4 years ago
Labels: cleanup

#44 - Chunyu/reads snps

Pull Request - State: closed - Opened by zhaoc1 almost 4 years ago

#43 - a couple major bugs fix and updates

Pull Request - State: closed - Opened by zhaoc1 over 4 years ago

#42 - workaround python multiprocessing map dispatch order

Pull Request - State: closed - Opened by boris-dimitrov over 4 years ago

#41 - port midas_merge_genes into iggtools

Pull Request - State: closed - Opened by zhaoc1 almost 5 years ago

#40 - port midas_merge_snps into iggtools

Pull Request - State: closed - Opened by zhaoc1 almost 5 years ago

#39 - Make `--sparse` act like a traditional option flag for run_midas_snps subcommand.

Pull Request - State: closed - Opened by bsmith89 almost 5 years ago - 3 comments