GMOD/jbrowse issues and pull requests

#1655 - Adding New Reference

Issue - State: closed - Opened by marcodimarsico 2 months ago - 2 comments

#1653 - Hi-C track: normalization and resolution

Issue - State: closed - Opened by ianakim 4 months ago

#1652 - node-modules folder is not created after running ./setup.sh

Issue - State: open - Opened by kostasgalexiou 4 months ago

#1651 - [Question] Is there a way to reduce number of files generated during indexing?

Issue - State: open - Opened by shreyas-a-s 6 months ago - 1 comment

#1650 - [Question] Is there any hideURIs option like JBrowse 2?

Issue - State: closed - Opened by shreyas-a-s 6 months ago - 2 comments

#1648 - Using a callback to set the height of sub-features is causing some of those features to be only partially-rendered

Issue - State: open - Opened by john-portwood 9 months ago - 6 comments

#1643 - Feature Request display CIGAR mismatch codes when zoomed out more

Issue - State: open - Opened by childers almost 2 years ago - 1 comment

#1642 - url controllable Highlighting in JB2

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

#1641 - Pangenome presence absence viz ?

Issue - State: open - Opened by colindaven almost 2 years ago - 2 comments

#1639 - Adding .bam and .bai from a server to the track.

Issue - State: closed - Opened by adaware-loxo almost 2 years ago - 3 comments

#1637 - Fix adding track in BioNanoGenomics plugins

Pull Request - State: open - Opened by cmdcolin almost 2 years ago

#1632 - Cannot install jbrowse-1.16.11-release developer version on macos ventura

Issue - State: open - Opened by thuynnguyen about 2 years ago - 1 comment

#1630 - Hello, I am testing to replace jbrowse with mouse data, but the tbi of the mouse gff3 file is always wrong here. I don't know what is wrong. I would like to ask you about the index. Do you have any mouse data to provide? ? thanks

Issue - State: open - Opened by ouyang-lang almost 3 years ago - 11 comments

#1629 - Tabix error

Issue - State: closed - Opened by francicco almost 3 years ago - 5 comments

#1627 - color of glyph

Issue - State: closed - Opened by srobb1 about 3 years ago - 6 comments

#1626 - Updating Node Deps

Pull Request - State: open - Opened by childers about 3 years ago - 1 comment

#1624 - XS.c: loadable library and perl binaries are mismatched (got handshake key 0xde00080, needed 0xcd00080)

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

#1619 - Problem with combination track, not working

Issue - State: open - Opened by armaos about 3 years ago - 10 comments

#1618 - Question: JB1 reference sequence alias?

Issue - State: closed - Opened by srobb1 over 3 years ago - 9 comments

#1617 - HTML linkouts in 1.16.11-release not rendering in the About this track panel

Issue - State: closed - Opened by childers over 3 years ago - 2 comments

#1616 - Links for older releases on the website are 404s

Issue - State: closed - Opened by kevinlul over 3 years ago - 5 comments

#1615 - ItemRgb not working for me

Issue - State: closed - Opened by srobb1 over 3 years ago - 6 comments

#1614 - SNPCoverage plots display fine with old laptop but not with new laptop

Issue - State: closed - Opened by Joseph-Vineland over 3 years ago - 7 comments

#1612 - Possible feature request

Issue - State: open - Opened by ValWood over 3 years ago - 4 comments

#1611 - Some question about y-axis scales on track

Issue - State: closed - Opened by ydy1127 over 3 years ago - 10 comments

#1610 - RequestError: Unable to load http://ip/jbrowse/JBrowse-1.16.11/data/CSV21/trackList.json?v=0.08820448948622106 status: 403.

Issue - State: closed - Opened by xiaoaozqd over 3 years ago - 8 comments

#1609 - onClick problem with URL

Issue - State: closed - Opened by mictadlo over 3 years ago - 7 comments

#1608 - Search by gene name

Issue - State: closed - Opened by fuzing over 3 years ago - 1 comment

#1607 - Remove node-sass to help avoid some install issues

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

#1606 - tab focus for accessibility enhancement?

Issue - State: open - Opened by mpoelchau over 3 years ago - 3 comments

#1605 - Update jbrowse 1 website header to refer to jbrowse 2

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

#1604 - What these values consist of "3a6/c61/ab" in the last end point when we hit hit track information......seq/3a6/c61/ab/110-38.txt ?

Issue - State: closed - Opened by sarimurrab over 3 years ago - 2 comments

#1603 - JBrowser configuration

Issue - State: closed - Opened by werhmk almost 4 years ago - 3 comments

#1602 - Bump hosted-git-info from 2.7.1 to 2.8.9 in /website

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 2 comments
Labels: dependencies

#1601 - Bump hosted-git-info from 2.8.8 to 2.8.9

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

#1600 - Bump lodash from 4.17.14 to 4.17.21 in /website

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

#1599 - Bump handlebars from 4.7.3 to 4.7.7

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

#1598 - Bump lodash from 4.17.15 to 4.17.21

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

#1597 - Bump url-parse from 1.4.3 to 1.5.1 in /website

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

#1596 - Feature start offset of one between Front-end and JS object

Issue - State: closed - Opened by Bjoernsen almost 4 years ago - 2 comments

#1595 - Available tracks window size

Issue - State: closed - Opened by demis001 almost 4 years ago - 5 comments

#1594 - Feature request: Absolute paths in configs

Issue - State: closed - Opened by Gogis0 almost 4 years ago - 4 comments

#1593 - reference sequence

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

#1592 - Bigwig XYplot

Issue - State: closed - Opened by demis001 almost 4 years ago - 11 comments

#1591 - JS class name of the glyph available options

Issue - State: closed - Opened by demis001 almost 4 years ago - 6 comments

#1590 - Update README.md to refer to jbrowse 2

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

#1589 - Failed to load resource: JBrowse/View/Track/Alignment2.

Issue - State: closed - Opened by JojoZhangxinye almost 4 years ago - 3 comments

#1587 - is there a way to organize a large number of datasets?

Issue - State: open - Opened by jvera888 almost 4 years ago - 2 comments

#1586 - Bump y18n from 3.2.1 to 3.2.2

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

#1585 - remove forward and back slashes from chunk filenames when formatting …

Pull Request - State: closed - Opened by rbuels almost 4 years ago - 11 comments

#1584 - Vhost SSL setting gave 403 error, http works

Issue - State: closed - Opened by demis001 almost 4 years ago - 2 comments

#1583 - Bump yargs-parser from 5.0.0 to 5.0.1

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

#1582 - Bump ini from 1.3.5 to 1.3.8

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

#1581 - Bump bl from 1.2.2 to 1.2.3

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

#1580 - Move jszlib dependency to util directory

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

#1579 - Bump elliptic from 6.5.2 to 6.5.4

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

#1578 - Question: align CanvasFeatures to the top

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

#1577 - Visualize multiple values per site in the same bigwig track

Issue - State: closed - Opened by yzhang2168 almost 4 years ago - 12 comments

#1576 - Bump prismjs from 1.15.0 to 1.23.0 in /website

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 2 comments
Labels: dependencies

#1575 - Save a static version Jbrowse on figshare

Issue - State: closed - Opened by Jungal10 almost 4 years ago - 4 comments

#1573 - Bump electron from 3.1.13 to 9.4.0

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

#1572 - Add a retry step to fetching features.

Pull Request - State: open - Opened by cmunk about 4 years ago - 2 comments

#1571 - Cannot be displayed on the external network

Issue - State: closed - Opened by dbx-git about 4 years ago - 8 comments

#1570 - JBrowse install on Mac Big Sur

Issue - State: closed - Opened by coralzhang about 4 years ago - 7 comments

#1569 - Bump @gmod/tabix for textdecoder speedup

Pull Request - State: closed - Opened by cmdcolin about 4 years ago

#1568 - Display of metrics and other information for gene models in JBrowse

Issue - State: closed - Opened by sanyalab about 4 years ago - 21 comments

#1567 - configure mouse click behavior using text based .conf

Issue - State: closed - Opened by billzt about 4 years ago - 2 comments

#1566 - Bump prismjs from 1.15.0 to 1.22.0 in /website

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

#1565 - Bump lodash from 4.17.14 to 4.17.20 in /website

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

#1564 - Bump ini from 1.3.5 to 1.3.8 in /website

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

#1562 - Bump bl from 1.2.2 to 1.2.3 in /website

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

#1558 - Deals with ACLs

Pull Request - State: open - Opened by FredericBGA about 4 years ago - 5 comments

#1557 - Bump highlight.js from 9.12.0 to 9.18.5 in /website

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

#1556 - adding annotation on a gff file results in uniqueID offset-1968619510"

Issue - State: open - Opened by Jungal10 over 4 years ago - 9 comments

#1555 - setup.sh yarn install fails - "Commit hash required"

Issue - State: closed - Opened by GFJHogue over 4 years ago - 4 comments

#1554 - Fix maker2jbrowse genespans

Pull Request - State: open - Opened by cmdcolin over 4 years ago

#1552 - How to use JBrowse when use the framework -- vue and webpack.

Issue - State: closed - Opened by linjiahao962889027 over 4 years ago - 2 comments

#1544 - Bump node-fetch from 2.6.0 to 2.6.1

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

#1543 - adding a little help text

Pull Request - State: open - Opened by scottcain over 4 years ago

#1542 - Some browser can not display the bam file

Issue - State: closed - Opened by Trandamere over 4 years ago - 10 comments

#1540 - syntaxError for gff file when gff is empty for current chromosome

Issue - State: closed - Opened by jjjscuedu over 4 years ago - 3 comments

#1537 - Bump prismjs from 1.15.0 to 1.21.0 in /website

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

#1534 - Bump elliptic from 6.5.2 to 6.5.3

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

#1532 - Bump lodash from 4.17.14 to 4.17.19 in /website

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

#1531 - Bump lodash from 4.17.15 to 4.17.19

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

#1527 - Bump electron from 3.1.13 to 7.2.4

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

#1526 - Error: jbrowse‘s index.html cannnot display

Issue - State: closed - Opened by AlexLc6 over 4 years ago - 6 comments

#1524 - Another Error: too may BAM features... question

Issue - State: closed - Opened by bioinfornatics over 4 years ago - 9 comments

#1522 - Can loops called from CHIA-PET/HI-CHIP data can be load into JBrower ？

Issue - State: closed - Opened by JiaoLaboratory over 4 years ago - 3 comments

#1517 - Bump dijit from 1.16.2 to 1.16.3

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

#1515 - Bump websocket-extensions from 0.1.3 to 0.1.4 in /website

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

#1511 - flatfile-to-json.pl --bed does not generate subfeatures anymore

Issue - State: open - Opened by mpoelchau over 4 years ago - 16 comments

#1504 - representing newlines in the track metadata

Issue - State: closed - Opened by mpoelchau over 4 years ago - 5 comments

#1477 - Allow generate-names.pl to index utf8 trackLabels

Pull Request - State: open - Opened by cmdcolin almost 5 years ago

#1472 - adding a build environment dockerfile for jbrowse

Pull Request - State: open - Opened by scottcain about 5 years ago - 4 comments

GitHub / GMOD/jbrowse issues and pull requests