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Recent Releases of basestack

basestack - 3.0.0

Version 3 of Basestack Beta Release.

Mac and Linux Users must execute the binary from the command line. For Example: ./Basestack.app/Contents/MacOS/Basestack for Mac and ./Basestack.x86_64.AppImage for Linux. This is due to restrictions to permissions in the $HOME directory for nextflow pipelines

Windows users are unaffected.

- JavaScript
Published by Merritt-Brian over 2 years ago

basestack - 2.4.7

  • Fixed a bug where a multi service job would skip ahead without waiting for the previous to complete

- JavaScript
Published by Merritt-Brian almost 3 years ago

basestack - 2.4.6

  • Fixed an issue where containers restarted due to Axios request timeout on Basestack Job submission
  • Updated database decompression targets for kraken2, allowing custom target locations of tarball decompression

- JavaScript
Published by Merritt-Brian almost 3 years ago

basestack - 2.4.5

  • Improve fetching of remote modules for individual pages (prioritize fetch over base library)
  • force tty on all docker containers run
  • Added estimated size attribute for dependencies
  • Set pulling of data with AXIOS for all types (http(s) and ftp)
  • Improve error reporting for downloading dependencies
  • Disable SSL verification for https pulls only

- JavaScript
Published by Merritt-Brian almost 3 years ago

basestack - 2.4.4

  • Fixed a bug on import not properly loading new module(s) due to async/promise issue
  • Allow an "autocheck/pull" toggle to automatically keep images up-to-date. This is able to be disabled.
  • More properly validate the bind mounts of certain files in list format to avoid improper string identifiers on container run

- JavaScript
Published by Merritt-Brian about 3 years ago

basestack - 2.4.3

  • Enable GPU support for Docker Containers
  • Fix Bug for failed retrieval of offline YAMLs causing improper module loading
  • Ignore Docker image digest values which caused issues with using loaded local versions

- JavaScript
Published by Merritt-Brian about 3 years ago

basestack - 2.4.2

  • Add ability to bind a list of paths for a given variable
  • Fixed Samplesheet bug where directories are not able to map appropriately for output purposes
  • Correctly report download percent for ftp, https downloads and appropriately cancel them

- JavaScript
Published by Merritt-Brian about 3 years ago

basestack - 2.4.1

  • Fix Nfcore_taxtriage failing on trimming
  • Fix bug where the output wasn't appropriately stated in the table
  • Allow periodic checking for new remote versions of modules

- JavaScript
Published by Merritt-Brian about 3 years ago

basestack - 2.4.0

  • No longer run Docker as user for Linux users
  • Added Medaka Module (Consensus)
  • Remote modules (in GitHub) are now opted as the "default" module on load
  • Correctly import modules available remotely, even if current version of Basestack does not package it

- JavaScript
Published by Merritt-Brian about 3 years ago

basestack - 2.3.9

Fixes: - Fix logs not showing properly for some jobs - Synchronize jobs now will print an alert message - Fixed Mytax2 demux for directories always occurring

Additions: - Adding a collapsible log viewer at the footer

- JavaScript
Published by Merritt-Brian about 3 years ago

basestack - 2.3.8

  • Fixed an issue with caching variables
  • adding the ability to open the path to a samplesheet.target.csv file
  • slight ui adjustment for variables

- JavaScript
Published by Merritt-Brian over 3 years ago

basestack - 2.3.7

Bug Fixes:

  • Archive icon to open folders/files now showing properly for input fields, including data table(s)
  • Permissions now appear for all files/folders of input fields
  • Improved coordination with input for mytax2

- JavaScript
Published by Merritt-Brian over 3 years ago

basestack - 2.3.6

Bug Fixes

  • Fixed an issue with unmapped, non bound paths

Features Added/Updated

  • Permission updater for files/directories
  • Adjusted UI
  • Removed Samplesheet needs

- JavaScript
Published by Merritt-Brian over 3 years ago

basestack - 2.3.5

Bug Fixes:

  • Relative to Absolute conversion of paths fixed from the front table
  • BOM removal for hidden characters in excel sheets are now accounted for. This would oftentimes omit columns of samplesheets

- JavaScript
Published by Merritt-Brian over 3 years ago

basestack - 2.3.4

Bug Fixes - Spaces and Dashes no longer cause issue with mounting volumes (Windows specifically) - Added a dry run option to all modules (log file output only, everything before pipeline starting for debug purposes)

- JavaScript
Published by Merritt-Brian over 3 years ago

basestack - 2.3.3

Bug Fixes - Minimap2: No output table present is now fixed - TaxTriage/Mytax2: Overriding the Samplesheet not properly working from the adjustable table - General Windows: Issues with spaces in pathing now fixed

- JavaScript
Published by Merritt-Brian over 3 years ago

basestack - 2.3.2

New Modules - Demultiplex

General Bug Fixes - Fixed an issue with scrolling throughout the main app

Upgrades/Changes - Adjusted positioning of output to make things more clear and apparent

Module Updates/Fixes - Mytax2: Adding ability to add custom bc files

- JavaScript
Published by Merritt-Brian over 3 years ago

basestack - 2.3.1

New Modules - Flye

General Bug Fixes - Fixed an issue where failed https downloads would report that the install was still ongoing

Upgrades/Changes - Added the ability to see data used per module

Module Updates/Fixes - Bowtie2 - Fixed output field option - Minimap2 - Fixed output field option - VADR - Fixed an issue with installing the necessary dependencies - IVAR - Fixed install issue for reference FASTA file - GAMMA - Fixed installation issue for AMR genes

- JavaScript
Published by Merritt-Brian over 3 years ago

basestack - 2.3.0

Bug Fixes - Fixed an error on a variable inside a container being defined even if empty or not used - Fixed an error for a multi option select that was simply a string

Features Updated/Changed - Added Samplesheet upload functionality to allow a multiple row and column bind of variables - Provided appropriate path resolving for more varied inputs, primarily for Windows benefits

- JavaScript
Published by Merritt-Brian over 3 years ago

basestack - 2.2.3

Bug Fixes

  • Fix Volume dependency checker for modules
  • Fix an issue with output not opening path in the module page

New Modules:

  • nfcore TaxTriage ( Private only, requires downloading separately)

- JavaScript
Published by Merritt-Brian over 3 years ago

basestack - 2.2.2

Bug Fixes

  1. Fixed an issue with defining variables if another one is updated
  2. Fixed an issue with trying to bind empty paths or non-absolutes

- JavaScript
Published by Merritt-Brian over 3 years ago

basestack - 2.2.1

Patch

  1. Fixed an issue on removing a module that is recently imported prior to app restart
  2. Allow Linux users to avoid having to use userns-remap from UI

- JavaScript
Published by Merritt-Brian over 3 years ago

basestack - 2.2.0

Pre Release for v2.2.0, please see v2.1.1 for the most up-to-date stable release

Changes in v2.2.0

  1. Further improved the multi-file input support
  2. Adjust module import order and process
  3. UI changes to modules and library
  4. Update several modules
    • IRMA
    • ViralRecon
    • Mytax

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian almost 4 years ago

basestack - 2.1.1

Pre Release for v2.1.1

Changelog

  • Patched Linux Orchestrator userns issues

New Docker Image(s) in v2.0

  • ViralRecon
  • IRMA
  • nanoplot
  • mash
  • ivar
  • vadr
  • minimap2
  • samtools (limited)
  • pangolin
  • unicycler
  • fastqc
  • agave
  • gamma
  • bamstats
  • medaka

Changes in v2.1.1

  1. Added Nextflow and Singularity Support in Dockerfile build of orchestrator
  2. Added ViralRecon Nanopore and Illumina Basic version
  3. Adjustable commands and custom input fields

Previous Changes in v2

  1. Improved UI design
  2. Improved interpretation of container orchestration for all pipelines
  3. Overhauled orchestration scheme, to utilize a more powerful pipeline framework
  4. Improved reporting methods (errors, status, etc)
  5. Allowed linking of multiple commands in a single procedure from multiple containers
  6. Added several modules (ivar, bamstats, gamma, unicycler, pangolin, fastqc, agave, vadr, minimap2)
  7. Patch env variable on passing strings or numbers
  8. Added numbers field to the UI
  9. Added medaka for consensus building scripts of SARS-CoV-2 using the Artic Primer schemes
  10. Add a second procedure to AGAVE to allow both ivar plus AGAVE in the same job
  11. Update required fields and notifications
  12. Correctly interpret non-complex entries from drop-down to update for value required validations
  13. Added MASH and NanoPlot
  14. Update Minimap2 to include sam to bam procedures
  15. Allow Docker Socket Adjustment for Linux Users Only
  16. Allow iVar (default) to use the consensus submodule

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian almost 4 years ago

basestack - 2.1.0

Pre Release for v2.1.0

Changelog

New Docker Image(s) in v2.0

  • ViralRecon
  • IRMA
  • nanoplot
  • mash
  • ivar
  • vadr
  • minimap2
  • samtools (limited)
  • pangolin
  • unicycler
  • fastqc
  • agave
  • gamma
  • bamstats
  • medaka

Changes in v2.1.0

  1. Added Nextflow and Singularity Support in Dockerfile build of orchestrator
  2. Added ViralRecon Nanopore and Illumina Basic version
  3. Adjustable commands and custom input fields

Previous Changes in v2

  1. Improved UI design
  2. Improved interpretation of container orchestration for all pipelines
  3. Overhauled orchestration scheme, to utilize a more powerful pipeline framework
  4. Improved reporting methods (errors, status, etc)
  5. Allowed linking of multiple commands in a single procedure from multiple containers
  6. Added several modules (ivar, bamstats, gamma, unicycler, pangolin, fastqc, agave, vadr, minimap2)
  7. Patch env variable on passing strings or numbers
  8. Added numbers field to the UI
  9. Added medaka for consensus building scripts of SARS-CoV-2 using the Artic Primer schemes
  10. Add a second procedure to AGAVE to allow both ivar plus AGAVE in the same job
  11. Update required fields and notifications
  12. Correctly interpret non-complex entries from drop-down to update for value required validations
  13. Added MASH and NanoPlot
  14. Update Minimap2 to include sam to bam procedures
  15. Allow Docker Socket Adjustment for Linux Users Only
  16. Allow iVar (default) to use the consensus submodule

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian almost 4 years ago

basestack - 2.0.5

Pre Release for v2.0.5

Changelog

New Docker Image(s) in v2.0

  • IRMA
  • nanoplot
  • mash
  • ivar
  • vadr
  • minimap2
  • samtools (limited)
  • pangolin
  • unicycler
  • fastqc
  • agave
  • gamma
  • bamstats
  • medaka

Changes in v2.0.5

  • Added irma
  • Give info for a server based on configuration (dialog)
  • Update versioning and control during services

Previous Changes in v2

  1. Improved UI design
  2. Improved interpretation of container orchestration for all pipelines
  3. Overhauled orchestration scheme, to utilize a more powerful pipeline framework
  4. Improved reporting methods (errors, status, etc)
  5. Allowed linking of multiple commands in a single procedure from multiple containers
  6. Added several modules (ivar, bamstats, gamma, unicycler, pangolin, fastqc, agave, vadr, minimap2)
  7. Patch env variable on passing strings or numbers
  8. Added numbers field to the UI
  9. Added medaka for consensus building scripts of SARS-CoV-2 using the Artic Primer schemes
  10. Add a second procedure to AGAVE to allow both ivar plus AGAVE in the same job
  11. Update required fields and notifications
  12. Correctly interpret non-complex entries from drop-down to update for value required validations
  13. Added MASH and NanoPlot
  14. Update Minimap2 to include sam to bam procedures
  15. Allow Docker Socket Adjustment for Linux Users Only
  16. Allow iVar (default) to use the consensus submodule

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian almost 4 years ago

basestack - 2.0.4

Changelog

New Docker Image(s) in v2.0

  • nanoplot
  • mash
  • ivar
  • vadr
  • minimap2
  • samtools (limited)
  • pangolin
  • unicycler
  • fastqc
  • agave
  • gamma
  • bamstats
  • medaka

Changes in v2.0.4

  • Allow Docker Socket Adjustment for Linux Users Only
  • Allow iVar (default) to use the consensus submodule
  • Fix some UI errors on overlapping the hint with the label for variables

Previous Changes in v2

  1. Improved UI design
  2. Improved interpretation of container orchestration for all pipelines
  3. Overhauled orchestration scheme, to utilize a more powerful pipeline framework
  4. Improved reporting methods (errors, status, etc)
  5. Allowed linking of multiple commands in a single procedure from multiple containers
  6. Added several modules (ivar, bamstats, gamma, unicycler, pangolin, fastqc, agave, vadr, minimap2)
  7. Patch env variable on passing strings or numbers
  8. Added numbers field to the UI
  9. Added medaka for consensus building scripts of SARS-CoV-2 using the Artic Primer schemes
  10. Add a second procedure to AGAVE to allow both ivar plus AGAVE in the same job
  11. Update required fields and notifications
  12. Correctly interpret non-complex entries from drop-down to update for value required validations
  13. Added MASH and NanoPlot
  14. Update Minimap2 to include sam to bam procedures

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian almost 4 years ago

basestack - 2.0.3

Changelog

New Docker Image(s) in v2.0

  • nanoplot
  • mash
  • ivar
  • vadr
  • minimap2
  • samtools (limited)
  • pangolin
  • unicycler
  • fastqc
  • agave
  • gamma
  • bamstats
  • medaka

Changes in v2.0.2

  • Add a second procedure to AGAVE to allow both ivar plus AGAVE in the same job
  • Update required fields and notifications
  • Correctly interpret non-complex entries from drop-down to update for value required validations
  • Added MASH and NanoPlot
  • Update Minimap2 to include sam to bam procedures

Previous Changes in v2

  1. Improved UI design
  2. Improved interpretation of container orchestration for all pipelines
  3. Overhauled orchestration scheme, to utilize a more powerful pipeline framework
  4. Improved reporting methods (errors, status, etc)
  5. Allowed linking of multiple commands in a single procedure from multiple containers
  6. Added several modules (ivar, bamstats, gamma, unicycler, pangolin, fastqc, agave, vadr, minimap2)
  7. Patch env variable on passing strings or numbers
  8. Added numbers field to the UI
  9. Added medaka for consensus building scripts of SARS-CoV-2 using the Artic Primer schemes

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian almost 4 years ago

basestack - 2.0.2

Changelog

New Docker Image(s) in v2.0

  • ivar
  • vadr
  • minimap2
  • samtools (limited)
  • pangolin
  • unicycler
  • fastqc
  • agave
  • gamma
  • bamstats
  • medaka

Changes in v2.0.2

  1. Patch env variable on passing strings or numbers
  2. Added numbers field to the UI
  3. Added medaka for consensus building scripts of SARS-CoV-2 using the Artic Primer schemes

Previous Changes in v2

  1. Improved UI design
  2. Improved interpretation of container orchestration for all pipelines
  3. Overhauled orchestration scheme, to utilize a more powerful pipeline framework
  4. Improved reporting methods (errors, status, etc)
  5. Allowed linking of multiple commands in a single procedure from multiple containers
  6. Added several modules (ivar, bamstats, gamma, unicycler, pangolin, fastqc, agave, vadr, minimap2)

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian almost 4 years ago

basestack - 2.0.1

Changelog

New Docker Image(s)

  • ivar
  • vadr
  • minimap2
  • samtools (limited)
  • pangolin
  • unicycler
  • fastqc
  • agave
  • gamma
  • bamstats

Changes in v2.0.1

  1. Patch for long-running jobs causing restarting of pipelines/services
  2. Adjusted Windows icon
  3. Provided ability to add more info for individual variables

Previous Changes in v2

  1. Improved UI design
  2. Improved interpretation of container orchestration for all pipelines
  3. Overhauled orchestration scheme, to utilize a more powerful pipeline framework
  4. Improved reporting methods (errors, status, etc)
  5. Allowed linking of multiple commands in a single procedure from multiple containers

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian almost 4 years ago

basestack - Nightly Jetson Build

THIS IS THE NIGHTLY BUILD for the JETSON NANO AND IS UNSTABLE AND UNDERGOING DEVELOPMENT

Please install the most up-to-date latest release: https://github.com/jhuapl-bio/Basestack/releases/latest if you need the amd64 variant that is stable for Mac, Linux, or Windows

- JavaScript
Published by Merritt-Brian about 4 years ago

basestack - 2.0.0

Stable Release for Basestack 2.0

- JavaScript
Published by Merritt-Brian about 4 years ago

basestack - 1.1.5

- JavaScript
Published by Merritt-Brian about 4 years ago

basestack - 1.1.4

Changelog

New Docker Image(s)

  • Mytax
  • Pavian
  • Oxford Demo

Changes in v1.1.4

  1. Updated Mytax Module to provide Centrifuge and Kraken2 support, remove deprecated Kraken v1

Previous Changes in v1

  1. Improved Developer Ecosystem for module additions
  2. Added Mytax
  3. Added Custom Database Processing for mytax reports
  4. Added Support alongside jhuaplbio/basestack_consensus to run artic-v4 primer sets
  5. Added Oxford Demo
  6. Provided GitHub Workflow for all 3 OS types
  7. Updated Banner Name for Oxford Seq Report Module

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian over 4 years ago

basestack - 1.1.3

Changelog

New Docker Image(s)

  • Mytax
  • Pavian
  • Oxford Demo

Changes in v1.1.3

  1. Updated Banner Name for Oxford Seq Report Module

Previous Changes in v1

  1. Improved Developer Ecosystem for module additions
  2. Added Mytax
  3. Added Custom Database Processing for mytax reports
  4. Added Support alongside jhuaplbio/basestack_consensus to run artic-v4 primer sets
  5. Added Oxford Demo
  6. Provided GitHub Workflow for all 3 OS types

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian over 4 years ago

basestack - v1.1.2

Changelog

New Docker Image(s)

  • Mytax
  • Pavian
  • Oxford Demo

Changes in v1.1.2

  1. Added Oxford Demo
  2. Provided GitHub Workflow for all 3 OS types

Previous Changes in v1

  1. Improved Developer Ecosystem for module additions
  2. Added Mytax
  3. Added Custom Database Processing for mytax reports
  4. Added Support alongside jhuaplbio/basestack_consensus to run artic-v4 primer sets

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian over 4 years ago

basestack - 1.1.1

Changelog

New Docker Image(s)

  • Mytax
  • Pavian

Changes in v1.1.1

  1. Added Custom Database Processing for mytax reports
  2. Added Support alongside jhuaplbio/basestack_consensus to run artic-v4 primer sets

Previous Changes in v1

  1. Improved Developer Ecosystem for module additions
  2. Added Mytax

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian over 4 years ago

basestack - 1.1.0

Changelog

New Docker Image(s)

  • Mytax
  • Pavian

Changes in v1.1.0

  1. Pavian

Previous Changes in v1

  1. Improved Developer Ecosystem for module additions
  2. Added Mytax

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian over 4 years ago

basestack - 1.0.0

Changelog

New Docker Image

  • Mytax

Changes in v1.0.0

  1. Improved Developer Ecosystem for module additions
  2. Added Mytax

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian over 4 years ago

basestack - 0.9.7

Changelog

Dockers to Update

  • Consensus (now v0.5.2)
    • Users may delete the original jhuaplbio/artic:latest image to save on space ## Linux
  • Users should follow the README documentation to setup Docker to allow subgid/subuid mapping or enable Docker Rootless here: https://github.com/jhuapl-bio/Basestack/#1-install-docker
  • Subsequent Updates will no longer show the version number in the binary name. Basestack.AppImage will now persist across updates.

Changes in v0.9.7

  1. Allow modification of run config and manifest mid-run
  2. Allow multiple barcode config files to be selected

Previous Changes in v0.9

  1. Fixed an issue that incorrectly notified of out-of-date modules
  2. Adding virtualization checking in System tab
  3. Fixed an issue with bash strict mode for RAMPART
  4. Notify if server port is in use for both development and production
  5. Notify if renderer port is in use for development mode only
  6. Add animation on fetching available Basestack version on startup
  7. Synchronized startup of app's components
  8. Build AppImage without version in productName
  9. Update to README for HyperV and WSL users
  10. Add Windows specific spawn/exec commands for installing WSL or enable HyperV
  11. Add feature to check if Docker installed
  12. Add private/public notification for module
  13. Fetch External Latest Digest, compare to local to see if module is out of date (Consensus only currently)
  14. Added ability to open Powershell or Terminal depending on OS
  15. Fixed a bug caused by incorrect calling of absolute pathing in Consensus module which broke report generation
  16. Provide ability to add custom primer schemes, barcoding, or basecalling cfg files/folders.
    • Please see https://artic.readthedocs.io/en/latest/primer-schemes/ for limitations in primer schemes, specifically naming
  17. Fixed a bug with rampart
  18. Transitioned the Docker Hub Repo for Consensus Generation
  19. Fix issue with copyfile from sequencing data to report path (if seq data is non-existent)
  20. Move default report path to sequencing run folder
  21. Update UI
  22. Do not require required files on bookmark for intermediate pipeline running (added warning if doing so)
  23. Fixed an issue where run_info caused an error during report generation (final step)
  24. Fix Docker Endpoint Changes not saving
  25. Add Endpoint Config in Install Page
  26. Minor Style changes
  27. Warn of multiple Seq Summary Presence (Breaks Module 4 of Basestack Consensus)
  28. Update Warning Messages

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian almost 5 years ago

basestack - 0.9.6

Changelog

Dockers to Update

  • Consensus (now v0.5.2)
    • Users may delete the original jhuaplbio/artic:latest image to save on space ## Linux
  • Users should follow the README documentation to setup Docker to allow subgid/subuid mapping or enable Docker Rootless here: https://github.com/jhuapl-bio/Basestack/#1-install-docker
  • Subsequent Updates will no longer show the version number in the binary name. Basestack.AppImage will now persist across updates.

Changes in v0.9.6

  1. Fix Docker Endpoint Changes not saving
  2. Add Endpoint Config in Install Page
  3. Minor Style changes
  4. Warn of multiple Seq Summary Presence (Breaks Module 4 of Basestack Consensus)
  5. Update Warning Messages

Previous Changes in v0.9

  1. Fixed an issue that incorrectly notified of out-of-date modules
  2. Adding virtualization checking in System tab
  3. Fixed an issue with bash strict mode for RAMPART
  4. Notify if server port is in use for both development and production
  5. Notify if renderer port is in use for development mode only
  6. Add animation on fetching available Basestack version on startup
  7. Synchronized startup of app's components
  8. Build AppImage without version in productName
  9. Update to README for HyperV and WSL users
  10. Add Windows specific spawn/exec commands for installing WSL or enable HyperV
  11. Add feature to check if Docker installed
  12. Add private/public notification for module
  13. Fetch External Latest Digest, compare to local to see if module is out of date (Consensus only currently)
  14. Added ability to open Powershell or Terminal depending on OS
  15. Fixed a bug caused by incorrect calling of absolute pathing in Consensus module which broke report generation
  16. Provide ability to add custom primer schemes, barcoding, or basecalling cfg files/folders.
    • Please see https://artic.readthedocs.io/en/latest/primer-schemes/ for limitations in primer schemes, specifically naming
  17. Fixed a bug with rampart
  18. Transitioned the Docker Hub Repo for Consensus Generation
  19. Fix issue with copyfile from sequencing data to report path (if seq data is non-existent)
  20. Move default report path to sequencing run folder
  21. Update UI
  22. Do not require required files on bookmark for intermediate pipeline running (added warning if doing so)
  23. Fixed an issue where run_info caused an error during report generation (final step)

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian almost 5 years ago

basestack - 0.9.5

Changelog

Dockers to Update

  • Consensus (now v0.5.2)
    • Users may delete the original jhuaplbio/artic:latest image to save on space ## Linux
  • Users should follow the README documentation to setup Docker to allow subgid/subuid mapping or enable Docker Rootless here: https://github.com/jhuapl-bio/Basestack/#1-install-docker
  • Subsequent Updates will no longer show the version number in the binary name. Basestack.AppImage will now persist across updates.

Changes in v0.9.5

  1. Fixed an issue where run_info caused an error during report generation (final step)

Previous Changes in v0.9

  1. Fixed an issue that incorrectly notified of out-of-date modules
  2. Adding virtualization checking in System tab
  3. Fixed an issue with bash strict mode for RAMPART
  4. Notify if server port is in use for both development and production
  5. Notify if renderer port is in use for development mode only
  6. Add animation on fetching available Basestack version on startup
  7. Synchronized startup of app's components
  8. Build AppImage without version in productName
  9. Update to README for HyperV and WSL users
  10. Add Windows specific spawn/exec commands for installing WSL or enable HyperV
  11. Add feature to check if Docker installed
  12. Add private/public notification for module
  13. Fetch External Latest Digest, compare to local to see if module is out of date (Consensus only currently)
  14. Added ability to open Powershell or Terminal depending on OS
  15. Fixed a bug caused by incorrect calling of absolute pathing in Consensus module which broke report generation
  16. Provide ability to add custom primer schemes, barcoding, or basecalling cfg files/folders.
    • Please see https://artic.readthedocs.io/en/latest/primer-schemes/ for limitations in primer schemes, specifically naming
  17. Fixed a bug with rampart
  18. Transitioned the Docker Hub Repo for Consensus Generation
  19. Fix issue with copyfile from sequencing data to report path (if seq data is non-existent)
  20. Move default report path to sequencing run folder
  21. Update UI
  22. Do not require required files on bookmark for intermediate pipeline running (added warning if doing so)

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian almost 5 years ago

basestack - 0.9.4

Changelog

Dockers to Update

  • Consensus (now v0.5.2)
    • Users may delete the original jhuaplbio/artic:latest image to save on space ## Linux
  • Users should follow the README documentation to setup Docker to allow subgid/subuid mapping or enable Docker Rootless here: https://github.com/jhuapl-bio/Basestack/#1-install-docker
  • Subsequent Updates will no longer show the version number in the binary name. Basestack.AppImage will now persist across updates.

Changes in v0.9.4

  1. Fix issue with copyfile from sequencing data to report path (if seq data is non-existent)
  2. Move default report path to sequencing run folder
  3. Update UI
  4. Do not require required files on bookmark for intermediate pipeline running (added warning if doing so)

Previous Changes in v0.9

  1. Fixed an issue that incorrectly notified of out-of-date modules
  2. Adding virtualization checking in System tab
  3. Fixed an issue with bash strict mode for RAMPART
  4. Notify if server port is in use for both development and production
  5. Notify if renderer port is in use for development mode only
  6. Add animation on fetching available Basestack version on startup
  7. Synchronized startup of app's components
  8. Build AppImage without version in productName
  9. Update to README for HyperV and WSL users
  10. Add Windows specific spawn/exec commands for installing WSL or enable HyperV
  11. Add feature to check if Docker installed
  12. Add private/public notification for module
  13. Fetch External Latest Digest, compare to local to see if module is out of date (Consensus only currently)
  14. Added ability to open Powershell or Terminal depending on OS
  15. Fixed a bug caused by incorrect calling of absolute pathing in Consensus module which broke report generation
  16. Provide ability to add custom primer schemes, barcoding, or basecalling cfg files/folders.
    • Please see https://artic.readthedocs.io/en/latest/primer-schemes/ for limitations in primer schemes, specifically naming
  17. Fixed a bug with rampart
  18. Transitioned the Docker Hub Repo for Consensus Generation

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian almost 5 years ago

basestack - 0.9.3

Changelog

Dockers to Update

  • Consensus (now v0.5.1)
    • Users may delete the original jhuaplbio/artic:latest image to save on space ## Linux
  • Users should follow the README documentation to setup Docker to allow subgid/subuid mapping or enable Docker Rootless here: https://github.com/jhuapl-bio/Basestack/#1-install-docker
  • Subsequent Updates will no longer show the version number in the binary name. Basestack.AppImage will now persist across updates.

Changes in v0.9.3

  1. Provide ability to add custom primer schemes, barcoding, or basecalling cfg files/folders.
    • Please see https://artic.readthedocs.io/en/latest/primer-schemes/ for limitations in primer schemes, specifically naming
  2. Fixed a bug with rampart
  3. Transitioned the Docker Hub Repo for Consensus Generation

Previous Changes in v0.9

  1. Fixed an issue that incorrectly notified of out-of-date modules
  2. Adding virtualization checking in System tab
  3. Fixed an issue with bash strict mode for RAMPART
  4. Notify if server port is in use for both development and production
  5. Notify if renderer port is in use for development mode only
  6. Add animation on fetching available Basestack version on startup
  7. Synchronized startup of app's components
  8. Build AppImage without version in productName
  9. Update to README for HyperV and WSL users
  10. Add Windows specific spawn/exec commands for installing WSL or enable HyperV
  11. Add feature to check if Docker installed
  12. Add private/public notification for module
  13. Fetch External Latest Digest, compare to local to see if module is out of date (Consensus only currently)
  14. Added ability to open Powershell or Terminal depending on OS
  15. Fixed a bug caused by incorrect calling of absolute pathing in Consensus module which broke report generation

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian almost 5 years ago

basestack - 0.9.2

Changelog

Dockers to Update

  • Consensus (now v0.4.0) ## Linux
  • Users should follow the README documentation to setup Docker to allow subgid/subuid mapping or enable Docker Rootless here: https://github.com/jhuapl-bio/Basestack/#1-install-docker
  • Subsequent Updates will no longer show the version number in the binary name. Basestack.AppImage will now persist across updates.

Changes in v0.9.2

  1. Fixed a bug caused by incorrect calling of absolute pathing in Consensus module which broke report generation

Previous Changes in v0.9

  1. Fixed an issue that incorrectly notified of out-of-date modules
  2. Adding virtualization checking in System tab
  3. Fixed an issue with bash strict mode for RAMPART
  4. Notify if server port is in use for both development and production
  5. Notify if renderer port is in use for development mode only
  6. Add animation on fetching available Basestack version on startup
  7. Synchronized startup of app's components
  8. Build AppImage without version in productName
  9. Update to README for HyperV and WSL users
  10. Add Windows specific spawn/exec commands for installing WSL or enable HyperV
  11. Add feature to check if Docker installed
  12. Add private/public notification for module
  13. Fetch External Latest Digest, compare to local to see if module is out of date (Consensus only currently)
  14. Added ability to open Powershell or Terminal depending on OS

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.9.1

Changelog

Dockers to Update

  • Consensus (now v0.4.0) ## Linux
  • Users should follow the README documentation to setup Docker to allow subgid/subuid mapping or enable Docker Rootless here: https://github.com/jhuapl-bio/Basestack/#1-install-docker
  • Subsequent Updates will no longer show the version number in the binary name. Basestack.AppImage will now persist across updates.

Changes in v0.9.1

  1. Fixed an issue that incorrectly notified of out-of-date modules
  2. Adding virtualization checking in System tab
  3. Fixed an issue with bash strict mode for RAMPART
  4. Notify if server port is in use for both development and production
  5. Notify if renderer port is in use for development mode only
  6. Add animation on fetching available Basestack version on startup
  7. Synchronized startup of app's components
  8. Build AppImage without version in productName

Previous Changes in v0.9.0

  1. Update to README for HyperV and WSL users
  2. Add Windows specific spawn/exec commands for installing WSL or enable HyperV
  3. Add feature to check if Docker installed
  4. Add private/public notification for module
  5. Fetch External Latest Digest, compare to local to see if module is out of date (Consensus only currently)
  6. Added ability to open Powershell or Terminal depending on OS

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.9.0

Changelog

Dockers to Update

  • Consensus (now v0.4.0) ## Linux
  • Users should follow the README documentation to setup Docker to allow subgid/subuid mapping here: https://github.com/jhuapl-bio/Basestack/#1-install-docker ## Mac
  • Users should reinstall the dmg file as it now allows auto-updating and suppresses the malicious software possibility warning ## Changes in v0.9.0
  1. Update to README for HyperV and WSL users
  2. Add Windows specific spawn/exec commands for installing WSL or enable HyperV
  3. Add feature to check if Docker installed
  4. Add private/public notification for module
  5. Fetch External Latest Digest, compare to local to see if module is out of date (Consensus only currently)
  6. Added ability to open Powershell or Terminal depending on OS

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.8.4

Changelog

Dockers to Update

  • Consensus (now v0.3.0) ## Linux
  • Users should follow the README documentation to setup Docker to allow subgid/subuid mapping here: https://github.com/jhuapl-bio/Basestack/#1-install-docker ## Mac
  • Users should reinstall the dmg file as it now allows auto-updating and suppresses the malicious software possibility warning ## Changes in v0.8.4
  • Redirect STDOUT/STDERR of containers to Docker logs file, useful for debugging
  • make drift correction and throughput files for Consensus module optional
  • Implement Nodemon Dev Server (Development only)

Previous v0.8 changes

  1. Open run folder directly on load
  2. Add 3 run specific file checks
  3. Add more error checking on permissions
  4. Added regex check for file presence
  5. Update Readme
  6. Improve UI
  7. Added changelog to homepage and as a request-able button
  8. Added open logs to service tray of the app
  9. Added Basestack Version to the System tab
  10. Fixed Mac auto-update & removed gatekeeper warning for malicious software possibility.
  11. Integrate Docker pull into consensus pipeline module build process
  12. Drop Down select run config and manifest items
  13. More information on run status and update modules
  14. Update module can be cancelled

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.8.3

Changelog

Dockers to Update

  • Consensus (now v0.3.0) ## Linux
  • Users should follow the README documentation to setup Docker to allow subgid/subuid mapping here: https://github.com/jhuapl-bio/Basestack/#1-install-docker ## Mac
  • Users should reinstall the dmg file as it now allows auto-updating and suppresses the malicious software possibility warning ## Changes in v0.8.3
  • Open run folder directly on load
  • Add 3 run specific file checks
  • Add more error checking on permissions
  • Added regex check for file presence
  • Update Readme
  • Improve UI

Previous v0.8 changes

  1. Added changelog to homepage and as a request-able button
  2. Added open logs to service tray of the app
  3. Added Basestack Version to the System tab
  4. Fixed Mac auto-update & removed gatekeeper warning for malicious software possibility.
  5. Integrate Docker pull into consensus pipeline module build process
  6. Drop Down select run config and manifest items
  7. More information on run status and update modules
  8. Update module can be cancelled

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.8.2

Changelog

Dockers to Update

  • Consensus (now v0.3.0) ## Linux
  • Users should follow the README documentation to setup Docker to allow subgid/subuid mapping here: https://github.com/jhuapl-bio/Basestack/#1-install-docker ## Mac
  • Users should reinstall the dmg file as it now allows auto-updating and suppresses the malicious software possibility warning ## Changes in v0.8.2
  • Drop Down select run config and manifest items
  • More information on run status and update modules
  • Update module can be cancelled

Previous v0.8 changes

  1. Added changelog to homepage and as a request-able button
  2. Added open logs to service tray of the app
  3. Added Basestack Version to the System tab
  4. Fixed Mac auto-update & removed gatekeeper warning for malicious software possibility.
  5. Integrate Docker pull into consensus pipeline module build process

Please see our Issue Tracker if you'd like to view upcoming changes, request a new feature, or notify us of a bug that needs fixing.

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.8.1

Changes 0.8.1

  1. Added changelog to homepage and as a request-able button
  2. Added open logs to service tray of the app
  3. Added Basestack Version to the System tab
  4. Fixed Mac auto-update & removed gatekeeper warning for malicious software possibility.

Previous 0.8 changes

  1. Integrate Docker pull into consensus pipeline module build process

Linux

  • Users should follow the README documentation to setup Docker to allow subgid/subuid mapping here: https://github.com/jhuapl-bio/Basestack/#1-install-docker

Mac

  • Users should reinstall the dmg file as it now allows auto-updating and suppresses the malicious software possibility warning

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.8.0

Version 0.8

  1. Docker Pull integration with Basestack Consensus

NOTE

  • Linux (only) Users must follow https://github.com/jhuapl-bio/Basestack/tree/staging#1-install-docker to setup Docker with new configurations

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.7.4

Changes in 0.7.4

  1. Only record fastq file count

Previous Changes in 0.7

  1. Fix Nextstrain not loading by adding a refresh button to refresh object
  2. Clear Fastq if invalid run selected in Consensus Tab

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.7.3

Changes 1. Nextstrain not loading initially 2. Remove the payload for large quantities of files between backend and UI/frontend 3. More Verbosity on Download Status or Completion

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.7.2

Adding Mac Zip as deliverable. Stay tuned for Release containing notarized signature for Windows and Mac. Currently, the app (on those platforms) must be run after accepting unverified publisher. Mac Auto-updater is currently non-functional

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.7.1

Hotfix for electron updater

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.7.0

Electron updater broke, hotfix incoming

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.6.0

Fix Rampart bug on starting due to change env. Drastically reduce consensus image size, update warnings for resources during build process.

- JavaScript
Published by Merritt-Brian about 5 years ago

basestack - 0.5.0

Initial release, Auto-updater foes not currently function properly. Mac DMG to come soon

- JavaScript
Published by Merritt-Brian about 5 years ago