allenday/nanostream-dataflow issues and pull requests

#98 - connection refused during alignment step

Issue - State: closed - Opened by lachlancoin almost 6 years ago - 3 comments

#97 - helper scripts for starting/closing

Issue - State: open - Opened by lachlancoin almost 6 years ago - 5 comments
Labels: tracked

#96 - add result separation by source folder

Pull Request - State: closed - Opened by pseveryn almost 6 years ago

#95 - add batch size and bwa arguments

Pull Request - State: closed - Opened by pseveryn almost 6 years ago

#94 - add fastq_splitter documentation. Utilities moved to separate dir

Pull Request - State: closed - Opened by pseveryn almost 6 years ago

#93 - Embed folder or .fastq name as part of Firestore document name

Issue - State: closed - Opened by Firedrops almost 6 years ago - 1 comment

#92 - add fastq splitter module

Pull Request - State: closed - Opened by pseveryn almost 6 years ago

#91 - gzip FastQ data before sending to the aligner

Issue - State: open - Opened by obsh almost 6 years ago
Labels: enhancement, tracked

#90 - add options for alignment batch size and for BWA arguments

Issue - State: closed - Opened by obsh almost 6 years ago - 1 comment
Labels: enhancement

#89 - Alignment cluster provisioning changes.

Pull Request - State: closed - Opened by obsh almost 6 years ago

#88 - Build 2019-02-21

Pull Request - State: closed - Opened by obsh almost 6 years ago

#87 - In visualization use colors from Firestore

Pull Request - State: closed - Opened by obsh almost 6 years ago

#86 - add taxonomy tree from file for resistant genes

Pull Request - State: closed - Opened by pseveryn almost 6 years ago

#85 - added colors to gene data. doc/2_Klebsiella.md fixes

Pull Request - State: closed - Opened by pseveryn almost 6 years ago

#84 - Updated visualizations to use data from the demo project.

Pull Request - State: closed - Opened by obsh almost 6 years ago

#83 - tests refactored. EndToEndTest improved

Pull Request - State: closed - Opened by pseveryn almost 6 years ago

#82 - create app engine front-end

Issue - State: closed - Opened by allenday almost 6 years ago
Labels: enhancement, tracked

#81 - provisioning node Server Error

Issue - State: closed - Opened by Firedrops almost 6 years ago - 1 comment

#80 - WIP. 2_Klebsiella example reproducibility.

Pull Request - State: closed - Opened by obsh almost 6 years ago

#79 - Visualization updated, minor fixes.

Pull Request - State: closed - Opened by obsh almost 6 years ago - 7 comments

#78 - #55 Integrate NCBI taxonomy from file

Pull Request - State: closed - Opened by obsh almost 6 years ago

#77 - refactored resistant genes Gene Info generation

Pull Request - State: closed - Opened by pseveryn almost 6 years ago

#76 - Back to try-catch in alignment step

Pull Request - State: closed - Opened by obsh almost 6 years ago

#75 - fixed problem with multiple result documents and changed project group id

Pull Request - State: closed - Opened by pseveryn almost 6 years ago

#74 - Single .fastq files generating multiple Firestore documents

Issue - State: closed - Opened by Firedrops almost 6 years ago - 1 comment

#73 - [Feature Request] Enable compatibility for .gz, maybe .cr files

Issue - State: open - Opened by Firedrops almost 6 years ago
Labels: enhancement, tracked

#72 - Pipeline still unstable with large .fastqs

Issue - State: open - Opened by Firedrops almost 6 years ago - 9 comments
Labels: tracked

#71 - New dogbite dataset spiked with publicly available reads

Issue - State: closed - Opened by lachlancoin almost 6 years ago - 3 comments

#70 - New databases available

Issue - State: closed - Opened by lachlancoin almost 6 years ago - 2 comments

#69 - namespace change

Issue - State: closed - Opened by allenday almost 6 years ago - 1 comment

#68 - sunburst resets to root view on refresh

Issue - State: open - Opened by allenday almost 6 years ago - 2 comments
Labels: enhancement, good first issue, tracked

#67 - make sunburst arc ordering deterministic

Issue - State: open - Opened by allenday almost 6 years ago - 3 comments
Labels: enhancement, good first issue, tracked

#66 - add pipeline commands for reproducibility

Issue - State: open - Opened by allenday almost 6 years ago - 1 comment
Labels: enhancement, tracked

#65 - Alignment adjustments. EndToEndPipelineTest skipped.

Pull Request - State: closed - Opened by obsh almost 6 years ago

#64 - refactor result naming

Pull Request - State: closed - Opened by pseveryn almost 6 years ago

#63 - provision.sh: HttpHealthCheck is deprecated

Issue - State: open - Opened by Firedrops almost 6 years ago - 1 comment
Labels: enhancement, tracked

#62 - Provisioning scripts cleanup (-c) jump to setup if firewall not found

Issue - State: closed - Opened by Firedrops almost 6 years ago - 1 comment
Labels: bug

#61 - Resistance pipeline ArrayIndexOutOfBoundsException

Issue - State: closed - Opened by Firedrops almost 6 years ago - 3 comments
Labels: bug

#60 - Aligner nodes memory 15 GB limitation?

Issue - State: closed - Opened by Firedrops almost 6 years ago - 8 comments
Labels: enhancement

#59 - Any interest in pubsub monitoring app?

Issue - State: closed - Opened by Firedrops almost 6 years ago - 4 comments
Labels: question

#58 - Logger misconfiguration

Issue - State: open - Opened by Firedrops almost 6 years ago - 5 comments
Labels: question, tracked

#57 - Add support for session partitioning of dataflow, support for folder-based multiplexing of processing.

Issue - State: open - Opened by obsh almost 6 years ago - 6 comments
Labels: enhancement, tracked

#56 - Document Firestore Permissions Setup

Issue - State: closed - Opened by obsh almost 6 years ago - 1 comment
Labels: enhancement, tracked

#55 - NCBI endpoint

Issue - State: closed - Opened by lachlancoin almost 6 years ago - 20 comments
Labels: enhancement

#54 - EndToEndPipelineTest Fails

Issue - State: closed - Opened by obsh almost 6 years ago - 3 comments
Labels: bug

#53 - Updated build

Pull Request - State: closed - Opened by obsh almost 6 years ago

#52 - remove Firestore Db argument, Readme.md edit

Pull Request - State: closed - Opened by pseveryn almost 6 years ago

#51 - Document Java version requirement

Issue - State: closed - Opened by obsh almost 6 years ago - 1 comment

#50 - Batch FastQ records before submitting request to aligner.

Pull Request - State: closed - Opened by obsh almost 6 years ago

#49 - Aligner cluster provisioning updates.

Pull Request - State: closed - Opened by obsh almost 6 years ago

#48 - Remove donut-chart

Pull Request - State: closed - Opened by obsh almost 6 years ago

#47 - add subscribtion creation description into README.md

Pull Request - State: closed - Opened by pseveryn almost 6 years ago

#46 - fix of https://github.com/allenday/nanostream-dataflow/issues/35 issue (source file path problem)

Pull Request - State: closed - Opened by pseveryn almost 6 years ago

#45 - Fixed "maven package" issues with OpenJDK.

Pull Request - State: closed - Opened by obsh almost 6 years ago

#44 - creating UPLOAD_EVENTS queue

Issue - State: closed - Opened by allenday almost 6 years ago - 1 comment

#43 - Factor out config in main README

Issue - State: closed - Opened by allenday almost 6 years ago - 1 comment

#42 - mvn -e clean package failing

Issue - State: closed - Opened by allenday almost 6 years ago - 4 comments

#41 - retrieve bwa files from prod location

Issue - State: closed - Opened by allenday almost 6 years ago - 4 comments

#40 - refactor app.js for visualization to function in prod location

Issue - State: open - Opened by allenday almost 6 years ago - 2 comments
Labels: bug, tracked

#39 - `docker run` fails for fasta_formatter

Issue - State: closed - Opened by allenday almost 6 years ago - 1 comment

#38 - fasta_formatter failing to build on dockerhub

Issue - State: closed - Opened by allenday almost 6 years ago - 4 comments

#37 - Create CODE_OF_CONDUCT.md

Pull Request - State: closed - Opened by allenday almost 6 years ago

#36 - Create LICENSE

Pull Request - State: closed - Opened by allenday almost 6 years ago

#35 - simulator README example fails

Issue - State: closed - Opened by allenday almost 6 years ago - 4 comments

#34 - replace error correction consensus local implemetation by japsa, refactoring

Pull Request - State: closed - Opened by pseveryn about 6 years ago - 1 comment

#33 - This resolves #32.

Pull Request - State: closed - Opened by obsh about 6 years ago

#32 - Configure Maven to create uber-jar

Issue - State: closed - Opened by obsh about 6 years ago

#31 - Use refactored 'consensusSequence' from Japsa

Issue - State: closed - Opened by obsh about 6 years ago - 2 comments

#30 - Added information regarding bucket with shared data.

Pull Request - State: closed - Opened by obsh about 6 years ago

#29 - Remove donut-chart

Issue - State: closed - Opened by obsh about 6 years ago

#28 - add multientity fastq file parsing

Pull Request - State: closed - Opened by pseveryn about 6 years ago

#27 - Generate CSS file for visualization from color scheme

Issue - State: closed - Opened by obsh about 6 years ago - 7 comments
Labels: enhancement

#26 - Docker missing apache2 SSLCertificateFile?

Issue - State: closed - Opened by Firedrops about 6 years ago - 2 comments

#25 - Visualization. Load js when document is ready. This fixes #22

Pull Request - State: closed - Opened by obsh about 6 years ago

#24 - Provide a color scheme for coloring bacterial species

Issue - State: closed - Opened by lachlancoin about 6 years ago - 2 comments

#23 - Help with pipeline command

Issue - State: closed - Opened by Firedrops about 6 years ago - 58 comments

#22 - How do I deploy the refactored visualization html?

Issue - State: closed - Opened by Firedrops about 6 years ago - 5 comments

#21 - How do I edit bwa-http-docker?

Issue - State: closed - Opened by Firedrops about 6 years ago - 1 comment

#20 - update readme

Pull Request - State: closed - Opened by pseveryn about 6 years ago

#19 - Visualization refactoring

Pull Request - State: closed - Opened by obsh about 6 years ago

#18 - move bucket to publication location, update permissions as "request pays"

Issue - State: closed - Opened by allenday about 6 years ago - 3 comments

#17 - made a lot of refactoring, added main Readme

Pull Request - State: closed - Opened by pseveryn about 6 years ago

#16 - implement multi-record reading for fastq files

Issue - State: closed - Opened by allenday about 6 years ago - 1 comment

#15 - Visualization added

Pull Request - State: closed - Opened by obsh about 6 years ago

#14 - add firestore output, taxonomy repository module, probe calculation

Pull Request - State: closed - Opened by pseveryn about 6 years ago

#13 - Gene info

Pull Request - State: closed - Opened by pseveryn about 6 years ago

#12 - add fasta formatter module

Pull Request - State: closed - Opened by pseveryn about 6 years ago

#11 - add error correction functionality, add tests

Pull Request - State: closed - Opened by pseveryn about 6 years ago

#10 - add kalign sequence alignment, DI with Guice, make some refactoring

Pull Request - State: closed - Opened by pseveryn about 6 years ago

#9 - Refactoring

Pull Request - State: closed - Opened by obsh about 6 years ago

#8 - fix all issues from review_2018_11_12

Pull Request - State: closed - Opened by pseveryn about 6 years ago

#7 - adopt simulator for fastq files emiting, make aligner part of pipeline

Pull Request - State: closed - Opened by pseveryn over 6 years ago

#6 - Provisioning scripts for alignment HTTP service

Pull Request - State: closed - Opened by obsh over 6 years ago

#5 - added part of dataflow app

Pull Request - State: closed - Opened by pseveryn over 6 years ago

#4 - added part of dataflow app

Pull Request - State: closed - Opened by pseveryn over 6 years ago - 1 comment

#3 - Simulator refactoring

Pull Request - State: closed - Opened by obsh over 6 years ago

#2 - Simulator fixing and refactoring

Pull Request - State: closed - Opened by pseveryn over 6 years ago

#1 - edit Docker file: fix google-cloud module, add google cloud credentia…

Pull Request - State: closed - Opened by pseveryn over 6 years ago

GitHub / allenday/nanostream-dataflow issues and pull requests