Releases: ohsu-comp-bio/funnel
0.11.0
Overview
This release adds support for version 1.1 of the TES schema as part of the GA4GH community.
Getting Started
See step by step guides on using Funnel to run and track tasks on the documentation page at https://ohsu-comp-bio.github.io/funnel
Installing
Homebrew
Funnel is available on macOS through Homebrew:
brew tap ohsu-comp-bio/formula
brew install funnel- Homebrew Formula: https://github.com/ohsu-comp-bio/homebrew-formula
- Docker image: https://quay.io/repository/ohsu-comp-bio/funnel?tab=tags
Install Script
Alternatively, Funnel may be installed with the installer script. By default it installs the latest release into the $HOME/.local/bin directory:
/bin/bash -c "$(curl -fsSL https://github.com/ohsu-comp-bio/funnel/releases/download/0.11.0/install.sh)"What's Changed
- TESv1.1 support
- Added initial Nextflow support
- Updated Homebrew installation and Docker images
Credits
Developed by the Ellrott Lab at Oregon Health & Science University.
Development was lead by Kyle Ellrott (@kellrott) with contributions from Alex Kanitz (@uniqueg), Adam Struck (@adamstruck), Adam Novak (@adamnovak), and Liam Beckman (@lbeckman314) with Data Analysis and HPC guidance by Jordan Lee (@jordan2lee).
Special thanks to Lakshya Garg (@LakiG) and Alex for their work on the TES Compliance Suite and to @bentsherman and @vsmalladi for continuing collaboration with Nextflow and TES on Azure.
Changelog
- PR #749 Add support for TES v1.1
- PR #761 Add Nextflow (nf-canary) tests to Funnel
- PR #724 Create dependabot.yml
Full Changelog: 0.10.1...0.11.0
Contributors
Assets 8
0.11.0-rc.5
356bead
lbeckman314
Liam Beckman
Overview
This release adds support for version 1.1 of the TES schema as part of the GA4GH community.
Getting Started
See step by step guides on using Funnel to run and track tasks on the documentation page at https://ohsu-comp-bio.github.io/funnel
Installing
Homebrew
Funnel is available on macOS through Homebrew:
brew tap ohsu-comp-bio/formula
brew install funnel- Homebrew Formula: https://github.com/ohsu-comp-bio/homebrew-formula
- Docker image: https://quay.io/repository/ohsu-comp-bio/funnel?tab=tags
Install Script
Alternatively, Funnel may be installed with the installer script. By default it installs the latest release into the $HOME/.local/bin directory:
/bin/bash -c "$(curl -fsSL https://github.com/ohsu-comp-bio/funnel/releases/download/0.11.0-rc.5/install.sh)" -- 0.11.0-rc.5What's Changed
- TESv1.1 support
- Added initial Nextflow support
- Updated Homebrew installation and Docker images
Credits
Developed by the Ellrott Lab at Oregon Health & Science University.
Development was lead by Kyle Ellrott (@kellrott) with contributions from Alex Kanitz (@uniqueg), Adam Struck (@adamstruck), Adam Novak (@adamnovak), and Liam Beckman (@lbeckman314) with Data Analysis and HPC guidance by Jordan Lee (@jordan2lee). Special thanks to Lakshya Garg (@LakiG) and Alex for their work on the TES Compliance Suite.
Changelog
Full Changelog: 0.10.1...0.11.0
Contributors
Assets 8
0.10.1
- PR #647 FIX: Open File leak
- PR #636 Updates for version 0.10.0
- PR #635 add .dockerignore
- PR #633 Adding new docker build
- PR #632 storage: add s3 presigned url support to https backend
- PR #626 Kubernetes Backend; Go Module Support
- PR #625 AWS Batch: limit methods used for resource creation
- PR #623 storage/s3: added sse-c and sse-kms support
- PR #619 worker: added config to limit parallel uploads/downloads
- PR #617 Optimize TaskStateCounts aggregate pipeline
- PR #613 docker: change base image tag; goreleaser: fix deprecation notices
- PR #612 database/mongodb: copy session for each op and maintain a connection pool
- PR #610 React web dashboard
0.10.0
- PR #636 Updates for version 0.10.0
- PR #635 add .dockerignore
- PR #633 Adding new docker build
- PR #632 storage: add s3 presigned url support to https backend
- PR #626 Kubernetes Backend; Go Module Support
- PR #625 AWS Batch: limit methods used for resource creation
- PR #623 storage/s3: added sse-c and sse-kms support
- PR #619 worker: added config to limit parallel uploads/downloads
- PR #617 Optimize TaskStateCounts aggregate pipeline
- PR #613 docker: change base image tag; goreleaser: fix deprecation notices
- PR #612 database/mongodb: copy session for each op and maintain a connection pool
- PR #610 React web dashboard
0.9.0
0.8.0
- PR #591 webdash: fix state filter bug
- PR #590 storage: more verbose errors
- PR #583 storage/local: fix directory list url join
- PR #581 allow multi-user basic auth
- PR #580 dynamodb: fix potential panic in tableIsAlive method
- PR #577 add version info when running 'make install'
- PR #576 webdash: optimize task list
- PR #575 build: use template for website download links
- PR #574 build: use external release notes builder
- PR #573 server: return WWW-Authenticate response header
- PR #572 compute/node: random node ID, use hostname in dashboard
- PR #571 database/mongo: add task state counts to service info
- PR #570 Fix typos in website
- PR #569 Update website
- PR #567 webdash: fix input/output description render; add created at column in task list
- PR #566 Typo
- PR #563 Fix HPC backend config templates on website
- PR #562 automatically get dependencies for 'tidy' and 'serve-doc' Makefile commands
- PR #561 database/badger: tweak retry timing
- PR #560 docs: example systemd service file for funnel node
- PR #559 Fix HPC templates in default-config.yaml
- PR #557 worker: use os/exec to connect to docker
- PR #556 databases: add Badger
- PR #555 Use dep to vendor dependencies
- PR #554 compute/manual: node draining
- PR #552 storage/swift: better retries and bug fixes
- PR #551 cmd/storage: add get and put
- PR #549 cmd/run: task field cleanup
Docker images
docker pull ohsucompbio/funnel:0.8.0
0.7.0
- PR #546 cmd/task/create: fix stdin pipe
- PR #544 tes: add task hash
- PR #542 web/dashboard: fix task list name overflow
- PR #540 cmd/run: remove "extra" args
- PR #535 webdash: fix syslog parser regex
- PR #533 cmd/task/create: read tasks from stdin
- PR #532 storage/swift: default chunk size of 500MB
- PR #530 config: handle error from ToYaml
- PR #529 config: fix duration flag parsing
- PR #528 config: use time.ParseDuration for duration strings
- PR #526 cmd: add completion command for bash completion
- PR #522 webdash: update url with filter params and keep after reload
Docker images
docker pull ohsucompbio/funnel:0.7.0
Automated with GoReleaser
Built with go version go1.10 darwin/amd64
0.6.2
0.6.1
- PR #519 webdash: fixed elapsedTime calculation
Docker images
docker pull ohsucompbio/funnel:0.6.1
Automated with GoReleaser
Built with go version go1.10 darwin/amd64
0.6.0
- PR #514 build: fix release notes command
- PR #513 Webdash upgrades
- PR #512 worker/docker: log container metadata
- PR #511 Unexport
- PR #510 build: goreleaser, 0.6.0, github release notes gen
- PR #508 fix for stdout/err log tail collection
- PR #507 auth: update default config and website docs
- PR #506 storage: use an io.Reader that utilizes context
- PR #505 server: configurable user for basic auth
- PR #502 databases: fix for task log metadata overwrite
- PR #501 worker: parallelize downloads and uploads
- PR #500 worker: always mount to /tmp in container
- PR #499 batch: fix nil panic when no resources are requested
- PR #498 Server run event writer initialization bug fix
- PR #492 dynamodb/datastore: syslogs in full task view
- PR #491 worker: more config options around stdout/err logging
- PR #489 server/elastic: fix tag filter to use keyword
- PR #488 compute/batch: fix panic when resources are requested
- PR #487 databases: added Init method to interface
- PR #486 api/cancel: handle event in compute backend first to allow for state check
- PR #483 api/tes: validate tags, require non-empty key
- PR #482 upgraded the databases to handle concurrent task state updates
- PR #471 api/tes: ListTask tag filters
- PR #469 use goimports to 'tidy' and 'lint' commands
- PR #467 webdash: debug/dev script
- PR #465 events/pubsub: google pub/sub event writer
- PR #464 compute/scheduler: fix node task cleanup restart edge case
- PR #461 storage: bug fixes
- PR #460 webdash: render newline in system logs
- PR #458 webdash: add all task fields
- PR #457 fix signal handling delay for cancelling the entrypoint context
- PR #455 compute/scheduler: fix nil panic on error log
- PR #454 logger/grpc: set most grpc logs to debug
- PR #453 api/tes: ListTasks state filter
- PR #446 server: correctly handle cancel event for manual backend
- PR #443 storage/local: directories were not downloaded correctly
- PR #441 build: remove unused github token
- PR #440 compute: reconcile task states with external queues
- PR #439 compute: cancel queued tasks; log failed Compute.Submit calls
- PR #438 Entrypoint cleanup; return an error from Worker.Run
- PR #437 grpc: less logging
- PR #436 test Scheduler.ReadQueue sort oder
- PR #435 mongo: ensure sort order; tests: check sort order
- PR #434 Vendor upgrade
- PR #431 worker/rpc: close rpc clients
Docker images
docker pull ohsucompbio/funnel:0.6.0
Automated with GoReleaser
Built with go version go1.10 darwin/amd64