Ecosyste.ms: Issues

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

GitHub / czbiohub/MIDAS2 issues and pull requests

#108 - merge_snps

Issue - State: open - Opened by luoqingqing777 about 1 year ago - 2 comments

#106 - bwa-meme

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

#105 - Update species_module.rst

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

#104 - Use bining data as ref-genome

Issue - State: open - Opened by BaylorLyu over 1 year ago - 2 comments

#103 - merge_snp issue still exist

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

#102 - how to build ughh database?

Issue - State: open - Opened by BaylorLyu almost 2 years ago - 1 comment

#101 - newdb related

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

#100 - Update glossary.rst

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

#99 - 2022 06 16/docs patch

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

#98 - Update glossary.rst

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

#97 - Update advanced_topics.rst

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

#96 - Update output.rst

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

#95 - Update output.rst

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

#94 - Update download_midasdb.rst

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

#93 - Update species_module.rst

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

#92 - Update overview.rst

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

#91 - Update quickstart.rst

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

#90 - 2022 06 15/rename midas2

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

#89 - add docs

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

#88 - merge_snps error

Issue - State: open - Opened by luoqingqing777 about 2 years ago - 8 comments

#87 - run_species error

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

#86 - midasdb gtdb alive on the server

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

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

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

#84 - midasdb uhgg ready on ucsf server

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

#83 - download failed

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

#82 - add md5sum check

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

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

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

#80 - v0.9.5

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

#79 - add ignore ambiguous sites

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

#78 - v0.9.3 migrate s3 bucket

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

#77 - add conda pkg recipe

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

#68 - major updates from large sample amounts

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

#67 - add analysis-ready option for bamfile

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

#66 - changes related to chunks and MIDASDB

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

#65 - pylint docker related updates

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

#64 - json int key into string

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

#63 - minor updates to the params

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

#62 - upgrade species flow from v0.33

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

#61 - update merge framework for v0.32

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

#60 - Chunyu/2021 08 31 species

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

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

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

#58 - Chunyu/2021 07 23 speed

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

#57 - minor updates for speed improvements

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

#56 - majors updates

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

#55 - major updates

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

#54 - update genes flow

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

#50 - minor change to build_bowtie2_db

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

#49 - update writing style in midas_merge_snps

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

#48 - add performance prints to unit test

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

#47 - exception handling in multiprocessing

Issue - State: closed - Opened by zhaoc1 over 3 years ago - 1 comment
Labels: help wanted, technical debt

#46 - add gene annotation to midas_merge_snps

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

#45 - [clean up] combine build_gene_features with annotate_genes

Issue - State: closed - Opened by zhaoc1 over 3 years ago
Labels: cleanup

#44 - Chunyu/reads snps

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

#43 - a couple major bugs fix and updates

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

#42 - workaround python multiprocessing map dispatch order

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

#41 - port midas_merge_genes into iggtools

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

#40 - port midas_merge_snps into iggtools

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

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

Pull Request - State: closed - Opened by bsmith89 over 4 years ago - 3 comments

#38 - Enable prebuilt bt2 db for midas_run_snps

Pull Request - State: open - Opened by bsmith89 over 4 years ago - 2 comments

#37 - Accept prefiltered MIDAS species list to midas_run_snps and midas_run_genes.

Pull Request - State: open - Opened by bsmith89 over 4 years ago - 1 comment

#36 - bowtie2-build non-zero exit does not propagate up to midas_run_genes subcommand

Issue - State: closed - Opened by bsmith89 over 4 years ago - 1 comment

#35 - add genome_info when clean import genomes

Issue - State: closed - Opened by zhaoc1 over 4 years ago - 1 comment

#34 - midas_merge_species ported to iggtools

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

#33 - add MIDAS shared analysis code to analysis/midas.py

Issue - State: closed - Opened by zhaoc1 over 4 years ago - 1 comment

#32 - Add user accessible threads parameter to midas_run subcommands.

Pull Request - State: open - Opened by bsmith89 over 4 years ago - 1 comment

#31 - Use no-sign-request flag when downloading from S3.

Pull Request - State: open - Opened by bsmith89 over 4 years ago - 6 comments

#30 - midas_run_snps ported to iggtools

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

#29 - move genes output dir a level up as originally intended

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

#28 - centroids.ffn clean up

Issue - State: closed - Opened by zhaoc1 over 4 years ago - 1 comment

#27 - `gene_info.txt` only for centroid genes for the future (

Issue - State: closed - Opened by zhaoc1 over 4 years ago - 1 comment

#26 - midas run_genes ported to iggtools

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

#25 - midas run_species workflow ported to iggtools

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

#24 - collate marker gene sequences for rep genomes

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

#23 - minor tweak to build_pangenomes

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

#22 - need to apply `temp` dir consistently

Issue - State: open - Opened by zhaoc1 over 4 years ago
Labels: technical debt

#21 - identify marker genes

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

#20 - annotate genes with prokka

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

#19 - import_uhgg

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

#18 - Boris/next2

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

#17 - support AWS instance types other than r5.12xlarge

Issue - State: open - Opened by boris-dimitrov over 4 years ago
Labels: technical debt

#16 - handle 99% clusters that do not contain their own centroids

Issue - State: closed - Opened by boris-dimitrov over 4 years ago - 2 comments
Labels: degenerate case

#15 - simplify submission of batch commands

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

#14 - allow running build_pangenome under aws batch

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

#10 - build_pangenome for single species

Pull Request - State: closed - Opened by boris-dimitrov over 4 years ago - 1 comment

#7 - mount nvme drives in aws_batch_init subcommand

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

#6 - python package subcommand structure and filesystem utils in docker

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

#2 - packaging for easy installation within batch container

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

#1 - Boris/docker

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