Ecosyste.ms: Issues

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

GitHub / databio/bedboss issues and pull requests

#85 - Speed improvements

Pull Request - State: open - Opened by khoroshevskyi 22 days ago

#84 - Bug in bedbuncher

Issue - State: open - Opened by khoroshevskyi 22 days ago

#83 - Improve reindexing

Issue - State: open - Opened by khoroshevskyi 22 days ago

#82 - check bed classifier

Issue - State: open - Opened by khoroshevskyi 23 days ago

#81 - Add validate config to bedboss

Issue - State: open - Opened by khoroshevskyi about 1 month ago

#80 - Add Rservice

Pull Request - State: open - Opened by nsheff about 2 months ago

#79 - Failing pipeline.

Issue - State: open - Opened by khoroshevskyi about 2 months ago

#78 - speed up bedboss / bedboss profiling

Issue - State: open - Opened by khoroshevskyi 2 months ago

#77 - Ref validator refactoring

Pull Request - State: closed - Opened by donaldcampbelljr 2 months ago

#76 - Release 0.4.1

Pull Request - State: closed - Opened by khoroshevskyi 3 months ago - 1 comment

#75 - Added new metadata model

Pull Request - State: closed - Opened by khoroshevskyi 3 months ago

#74 - Dev ref genome validator

Pull Request - State: closed - Opened by nsheff 3 months ago

#73 - Release 0.4.0

Pull Request - State: closed - Opened by khoroshevskyi 3 months ago

#72 - integrate populator repository

Issue - State: closed - Opened by nsheff 9 months ago - 2 comments

#71 - added bbuploader

Pull Request - State: closed - Opened by khoroshevskyi 3 months ago

#69 - Next steps

Issue - State: closed - Opened by khoroshevskyi 4 months ago - 1 comment

#68 - Avoiding 403s

Issue - State: closed - Opened by jwokaty 4 months ago - 1 comment

#67 - Dev bedclassifier script

Pull Request - State: closed - Opened by donaldcampbelljr 6 months ago - 2 comments

#66 - Add license field to uploading bed files

Issue - State: closed - Opened by khoroshevskyi 6 months ago - 1 comment

#65 - Add uploading bed tokens

Issue - State: closed - Opened by khoroshevskyi 6 months ago - 1 comment

#64 - Add function for uploading bed tokens

Issue - State: closed - Opened by khoroshevskyi 6 months ago - 1 comment

#63 - release 0.3.0

Pull Request - State: closed - Opened by khoroshevskyi 7 months ago

#62 - Should we standardize bed files?

Issue - State: open - Opened by khoroshevskyi 8 months ago - 2 comments
Labels: question, high-priority

#61 - Release 0.2.1

Pull Request - State: closed - Opened by khoroshevskyi 8 months ago

#60 - Improve BED Classifier

Issue - State: open - Opened by donaldcampbelljr 8 months ago - 2 comments

#58 - Where should metadata live?

Issue - State: open - Opened by khoroshevskyi 8 months ago - 1 comment
Labels: enhancement, brainstorming

#57 - v0.2.0

Pull Request - State: closed - Opened by khoroshevskyi 8 months ago

#56 - New bbconf

Pull Request - State: closed - Opened by khoroshevskyi 8 months ago

#55 - bedset - create new statistics and metadata

Issue - State: open - Opened by khoroshevskyi 8 months ago

#54 - Bedboss: Consolidating bedbase pipeline components

Issue - State: closed - Opened by nsheff about 2 years ago - 2 comments
Labels: brainstorming

#53 - Update cli

Issue - State: closed - Opened by khoroshevskyi 9 months ago - 1 comment

#52 - Bed cache

Pull Request - State: closed - Opened by khoroshevskyi 9 months ago

#51 - Update qdrant

Issue - State: closed - Opened by khoroshevskyi 9 months ago - 2 comments

#50 - Update bedset

Issue - State: closed - Opened by khoroshevskyi 9 months ago - 1 comment

#49 - Add S3 upload check if file exists in the bucket

Issue - State: closed - Opened by khoroshevskyi 9 months ago - 1 comment
Labels: enhancement, wontfix

#48 - Bedqc: improving bedqc filter

Issue - State: open - Opened by xuebingjie1990 almost 2 years ago
Labels: brainstorming

#47 - Ensure bedboss uses pipestat > v0.4.0

Issue - State: closed - Opened by donaldcampbelljr over 1 year ago - 1 comment

#46 - Clean bedstat

Issue - State: closed - Opened by khoroshevskyi 9 months ago

#45 - Update README.md

Pull Request - State: closed - Opened by khoroshevskyi 9 months ago

#44 - Restructuring

Pull Request - State: closed - Opened by khoroshevskyi 9 months ago

#44 - Restructuring

Pull Request - State: closed - Opened by khoroshevskyi 9 months ago

#43 - Check if bedboss is producing correct digest

Issue - State: closed - Opened by khoroshevskyi 9 months ago - 1 comment

#42 - improve bedqc error raising

Issue - State: closed - Opened by khoroshevskyi 9 months ago

#42 - improve bedqc error raising

Issue - State: closed - Opened by khoroshevskyi 9 months ago

#41 - clean up CLI of bedboss

Issue - State: closed - Opened by khoroshevskyi 9 months ago

#40 - Restructuring

Pull Request - State: closed - Opened by khoroshevskyi 9 months ago

#39 - Update bed classifier

Pull Request - State: closed - Opened by donaldcampbelljr 9 months ago - 1 comment

#38 - Bed files and statistics should be named according to their digest.

Issue - State: closed - Opened by khoroshevskyi 9 months ago - 1 comment

#36 - bedboss should use bbclient!

Issue - State: closed - Opened by khoroshevskyi 10 months ago - 2 comments
Labels: enhancement

#35 - Add Bed Classifier

Pull Request - State: closed - Opened by donaldcampbelljr 10 months ago - 1 comment

#34 - Specify different flavors of BED

Issue - State: closed - Opened by nsheff 11 months ago - 20 comments

#33 - Allow uploading meta data from input pep to an output pep via registry path

Pull Request - State: closed - Opened by donaldcampbelljr 10 months ago - 1 comment

#32 - Use pephubclient to create new bedset, as View

Issue - State: closed - Opened by khoroshevskyi 10 months ago

#31 - Use pephubclient to upload bed metadata as PEP sample

Issue - State: closed - Opened by khoroshevskyi 10 months ago - 4 comments

#30 - All pytest currently errors with: OSError: [Errno 29] Illegal seek

Issue - State: closed - Opened by donaldcampbelljr 10 months ago - 2 comments
Labels: likely-solved

#29 - Bedbase PEP schema in pephub

Issue - State: closed - Opened by khoroshevskyi 10 months ago - 10 comments

#27 - add bedboss tests

Issue - State: closed - Opened by khoroshevskyi 11 months ago - 1 comment

#26 - Create package that will project (store) information about s3 storage

Issue - State: closed - Opened by khoroshevskyi 12 months ago - 3 comments
Labels: enhancement, brainstorming, high-priority

#25 - Add checking Refgenie in env vars

Issue - State: closed - Opened by khoroshevskyi 12 months ago

#24 - Add documentation

Issue - State: closed - Opened by khoroshevskyi 12 months ago - 1 comment

#23 - install checker is too slow with R packages

Issue - State: open - Opened by nsheff 12 months ago
Labels: enhancement, help wanted

#22 - Add pephub, as online source for bedboss-all and stats

Issue - State: closed - Opened by khoroshevskyi about 1 year ago - 1 comment
Labels: likely-solved

#21 - Release v0.1.0

Pull Request - State: closed - Opened by khoroshevskyi about 1 year ago - 1 comment

#20 - Add bedbuncher to bedboss

Issue - State: closed - Opened by khoroshevskyi about 1 year ago
Labels: enhancement, likely-solved

#19 - Add qdrant upload function

Issue - State: closed - Opened by khoroshevskyi about 1 year ago
Labels: enhancement, likely-solved

#18 - Add metadata while inserting bedfile to db.

Issue - State: closed - Opened by khoroshevskyi about 1 year ago - 2 comments
Labels: enhancement, likely-solved

#17 - Release 0.1.0a4

Pull Request - State: closed - Opened by khoroshevskyi about 1 year ago

#16 - v0.1.0a3

Pull Request - State: closed - Opened by khoroshevskyi about 1 year ago

#15 - Adding qdrant uploader

Pull Request - State: closed - Opened by khoroshevskyi about 1 year ago

#14 - output schema

Issue - State: closed - Opened by nsheff about 1 year ago - 2 comments

#13 - R 'caught an error!' message

Issue - State: closed - Opened by nsheff about 1 year ago - 2 comments
Labels: likely-solved

#12 - R package check is broken

Issue - State: closed - Opened by nsheff about 1 year ago - 3 comments

#11 - Create an input schema for bedboss insert

Issue - State: closed - Opened by khoroshevskyi over 1 year ago - 2 comments
Labels: likely-solved

#10 - Dev

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

#9 - Use new lab secrets approach

Issue - State: closed - Opened by nsheff over 1 year ago - 2 comments
Labels: likely-solved

#8 - Bedstat overwrite db

Pull Request - State: closed - Opened by xuebingjie1990 almost 2 years ago - 1 comment

#7 - New tests and documentation

Pull Request - State: closed - Opened by khoroshevskyi almost 2 years ago

#6 - Switching the CLI from an argument-based parameterization to a config-based parameterization

Issue - State: closed - Opened by khoroshevskyi almost 2 years ago - 2 comments
Labels: brainstorming

#5 - added new cli

Pull Request - State: closed - Opened by khoroshevskyi almost 2 years ago

#4 - Improve bedmaker

Pull Request - State: closed - Opened by xuebingjie1990 almost 2 years ago

#3 - Create an output schema

Issue - State: closed - Opened by nsheff almost 2 years ago - 1 comment

#2 - v0.1.0a1

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

#1 - Check programs and scripts needed for running bedboss

Issue - State: closed - Opened by khoroshevskyi almost 2 years ago - 2 comments
Labels: dependencies