Ecosyste.ms: Issues

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

GitHub / ginkgobioworks/edge issues and pull requests

#102 - Bump django from 2.2.20 to 3.2.24

Pull Request - State: open - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#101 - SSR Annotation Handling

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

#100 - Change BLAST word size default to 11, add optional arg in BLAST/PCR API

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

#99 - Recombine and SSR now accept empty annotation lists

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

#98 - Bump flower from 0.9.2 to 1.2.0

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#97 - Create SSR UI

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

#96 - add sequence to feature and option to get in api

Pull Request - State: closed - Opened by Lioscro almost 2 years ago - 3 comments

#95 - return template annotations from pcr

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

#93 - Support ssr

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

#92 - Create API for getting coordinates of diff between child and parent genomes

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

#91 - Patch Reference-based Fasta Export

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

#90 - fixed flake8, bumped version to 3.25.1

Pull Request - State: closed - Opened by alecethell about 2 years ago

#89 - Create Export FASTA API

Pull Request - State: closed - Opened by alecethell about 2 years ago - 1 comment

#88 - Bump numpy from 1.12.1 to 1.22.0

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#87 - Implement reference-based chunks

Pull Request - State: closed - Opened by alecethell about 2 years ago

#86 - Bump django from 2.2.20 to 2.2.28

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#85 - Bump numpy from 1.12.1 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#84 - order the fragments when we make genome indicies, to may be avoid dea…

Pull Request - State: closed - Opened by benjiec over 2 years ago

#83 - Bump django from 2.2.20 to 2.2.27

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#82 - Bump celery from 4.1.0 to 5.2.2

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#81 - None strand GFF import fix

Pull Request - State: closed - Opened by alecethell over 2 years ago

#80 - all annotation types now default to "misc"

Pull Request - State: closed - Opened by alecethell over 2 years ago

#79 - updated README

Pull Request - State: closed - Opened by benjiec over 2 years ago

#78 - Bump django from 2.2.20 to 2.2.25

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#77 - further reduce race condition: better fragment locking, moving delaye…

Pull Request - State: closed - Opened by benjiec over 2 years ago

#76 - add a select_for_update lock

Pull Request - State: closed - Opened by benjiec over 2 years ago

#75 - allow insertion of sequences without deletion via hr

Pull Request - State: closed - Opened by benjiec over 2 years ago

#73 - construct fasta using tempfile and construct separate blastdb per db …

Pull Request - State: closed - Opened by benjiec over 2 years ago

#72 - improved subfeature importing, wrap around circular end features

Pull Request - State: closed - Opened by alecethell over 2 years ago

#71 - bump bc-bio and add some tests

Pull Request - State: closed - Opened by benjiec over 2 years ago

#70 - Use v0.6.7 of bcbio-gff

Pull Request - State: closed - Opened by raymond-lam almost 3 years ago

#68 - if server is a ro server, and requires location index or genome DB, f…

Pull Request - State: closed - Opened by benjiec almost 3 years ago

#67 - Test annotation on reverse strand

Pull Request - State: closed - Opened by benjiec almost 3 years ago

#66 - Include Subfeatures in GFF Export

Pull Request - State: closed - Opened by alecethell almost 3 years ago

#65 - resolved flake8 syntax marks for importer, test_importer, and recombine

Pull Request - State: closed - Opened by alecethell almost 3 years ago

#64 - Import CDS "join" subfragments from GFF

Pull Request - State: closed - Opened by alecethell almost 3 years ago - 1 comment

#63 - Update PyPI token username

Pull Request - State: closed - Opened by bhyman about 3 years ago - 1 comment

#62 - Revert "Publish to PyPi via GitHub Actions (#59)"

Pull Request - State: closed - Opened by bhyman about 3 years ago - 2 comments

#61 - Testing Travis builds on PRs

Pull Request - State: closed - Opened by bhyman about 3 years ago

#60 - Add Bower CI/CD dependency

Pull Request - State: open - Opened by bhyman about 3 years ago

#59 - Publish to PyPi via GitHub Actions

Pull Request - State: closed - Opened by bhyman about 3 years ago

#58 - Update FullStory CDN link, recording snippet

Pull Request - State: closed - Opened by bhyman about 3 years ago

#57 - Bump django from 2.2.20 to 2.2.24

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#56 - Bump django from 2.2.20 to 2.2.22

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#55 - Bump django from 2.2.20 to 2.2.21

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#54 - return feature information, along with annotations

Pull Request - State: closed - Opened by benjiec about 3 years ago - 2 comments

#53 - supports annotation of multiple chunks under one annotation

Pull Request - State: closed - Opened by benjiec about 3 years ago

#52 - Add code formatters

Pull Request - State: closed - Opened by Chris7 about 3 years ago - 3 comments

#51 - Add ability to derive a new genome from adding a fragment

Pull Request - State: closed - Opened by Chris7 about 3 years ago

#50 - Update dependencies

Pull Request - State: closed - Opened by jamieleecho about 3 years ago

#49 - schedule task to build genome index if one is not available

Pull Request - State: closed - Opened by benjiec about 3 years ago

#48 - Bump django from 2.2.10 to 2.2.20

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#47 - Bump django from 2.2.10 to 2.2.18

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#46 - Allow annotation of donor DNA when doing a HR

Pull Request - State: closed - Opened by benjiec over 3 years ago

#44 - completely removing evalue param from blast

Pull Request - State: closed - Opened by benjiec over 3 years ago - 3 comments

#43 - on large import of a genome w/o any annotation, divide up only chunk …

Pull Request - State: closed - Opened by benjiec almost 4 years ago - 2 comments

#42 - Large import

Pull Request - State: closed - Opened by benjiec almost 4 years ago

#41 - Bump django from 2.2.10 to 2.2.13

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies

#40 - fix import and mostly export GFF woes

Pull Request - State: closed - Opened by benjiec over 4 years ago

#39 - add qualifiers from JSON API to annotation

Pull Request - State: closed - Opened by benjiec over 4 years ago

#38 - Bump django from 2.2.8 to 2.2.10

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago
Labels: dependencies

#37 - fix multiple recombinations on multiple fragments

Pull Request - State: closed - Opened by benjiec over 4 years ago - 1 comment

#36 - Bump django from 2.2.6 to 2.2.8

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago
Labels: dependencies

#35 - Add queryset evaluation to actually lock root genome

Pull Request - State: closed - Opened by yaoyuyang over 4 years ago - 1 comment

#34 - Setup fullstory recording

Pull Request - State: closed - Opened by yaoyuyang over 4 years ago - 2 comments

#33 - Lock root genome to prevent genomes recombination corruption

Pull Request - State: closed - Opened by yaoyuyang over 4 years ago - 1 comment

#32 - Update python

Pull Request - State: closed - Opened by jamieleecho almost 5 years ago

#31 - Update packages

Pull Request - State: closed - Opened by jamieleecho almost 5 years ago - 2 comments

#30 - Update Dockerfile to enable npm setup

Pull Request - State: closed - Opened by yaoyuyang about 5 years ago - 1 comment

#29 - Fix export for negative strand

Pull Request - State: closed - Opened by Chris7 over 5 years ago

#28 - Search annotation by qualifiers

Pull Request - State: closed - Opened by benjiec over 5 years ago - 6 comments

#27 - Upgrade bcbio gff to 0.6.4

Pull Request - State: closed - Opened by yaoyuyang about 6 years ago - 2 comments

#26 - Upgrade bcbio to 0.6.4 to reduce import gff errors

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

#25 - Improve Edge error message return for import genome

Issue - State: open - Opened by yaoyuyang about 6 years ago

#24 - Last modified date

Issue - State: open - Opened by Chris7 over 6 years ago

#23 - Remove name for shared_task so that it uses edge.tasks.xxx as name

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

#22 - Add refresh option for build_fragment_fasta

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

#21 - Add an option to force rebuild blastdb for fragments

Issue - State: closed - Opened by yaoyuyang over 6 years ago - 1 comment

#20 - EDGE show sequence needs to have a better format

Issue - State: open - Opened by yaoyuyang over 6 years ago

#19 - Upgrade celery to 4.1.0 and flower to 0.9.2

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

#18 - Upgrade celery to 4.1.0

Issue - State: closed - Opened by yaoyuyang over 6 years ago - 1 comment

#17 - Fix some issues with genomic PCR

Pull Request - State: closed - Opened by benjiec over 6 years ago - 5 comments

#16 - Import gff ui

Pull Request - State: closed - Opened by yaoyuyang over 6 years ago - 7 comments

#15 - Upgrade webassets to deal with Django upgrade

Pull Request - State: closed - Opened by myw over 6 years ago
Labels: bug

#14 - Upgrade to Django 1.11

Pull Request - State: closed - Opened by Chris7 over 6 years ago

#13 - Update readme to include using docker-compose directly

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

#12 - Recombination doesn't work with docker-compose setup

Issue - State: closed - Opened by yaoyuyang over 6 years ago

#11 - Set up rabbit in docker-compose and use in app

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

#10 - Add an import genome button

Issue - State: closed - Opened by yaoyuyang over 6 years ago - 2 comments
Labels: enhancement

#9 - Fix export button link bug

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

#8 - Add the fix for syncdb

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

#7 - Wait for database to bootup before run server

Issue - State: closed - Opened by yaoyuyang over 6 years ago - 1 comment

#6 - Added Edge export button

Pull Request - State: closed - Opened by aruginkgo almost 7 years ago - 5 comments

#5 - Edge export button

Pull Request - State: closed - Opened by aruginkgo almost 7 years ago - 1 comment

#4 - More descriptive annotation needed from Edge

Issue - State: open - Opened by lfaller almost 7 years ago

#3 - Add button in UI to export edge genome to gff file

Issue - State: closed - Opened by yaoyuyang about 7 years ago - 1 comment