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
#107 - merge function writing chunks in database folder which may not be writeable
Issue -
State: open - Opened by FranckLejzerowicz over 1 year ago
- 4 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