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Add JBrowse2#6021

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bgruening wants to merge 215 commits intogalaxyproject:maingalaxyproject/tools-iuc:mainfrom bgruening:jb2rebased_mainbgruening/tools-iuc:jb2rebased_mainCopy head branch name to clipboard

+12,860

Commits

Commits on May 21, 2024

• Jbrowse2 tool, still wip

  

  abretaud

  authored and

  bgruening

  committed
  0eabcdc

• fix

  

  abretaud

  authored and

  bgruening

  committed
  71ff77a

• update to 1.6.4

  

  abretaud

  authored and

  bgruening

  committed
  9028aba

• remove the standalone option, not very useful for jbrowse2

  

  abretaud

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  committed
  cbac152

• genetic code not available yet

  

  abretaud

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  0fefb89

• sparql

  

  abretaud

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  96a2bc0

• sparql

  

  abretaud

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  2df4afb

• add synteny track

  

  abretaud

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  d04b003

• add cram

  

  abretaud

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  04a72bb

• add vcf_bgzip

  

  abretaud

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  edd06cf

• auto conversion does the job

  

  abretaud

  authored and

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  committed
  8e17b46

• add hic

  

  abretaud

  authored and

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  committed
  78cd9e1

• add default session + general options

  

  abretaud

  authored and

  bgruening

  committed
  91e781d

• update citation

  

  abretaud

  authored and

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  committed
  b79cae1

• Some progress to preconfigure a default session with default tracks and some track rendering options. Half broken/not finished

  

  abretaud

  authored and

  bgruening

  committed
  80f1c91

• Run code through black

  

  hexylena

  authored and

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  committed
  b4c7027

• Import Ross's changes

  Show description for e7d61a5
  

  fubar2

  authored and

  bgruening

  committed
  e7d61a5

• Everything required for assemblies.

  

  hexylena

  authored and

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  committed
  0f0ca09

• The python version is mostly whitespace

  

  hexylena

  authored and

  bgruening

  committed
  9f30129

• working default behaviour

  

  hexylena

  authored and

  bgruening

  committed
  7a5ea4a

• optional cwd

  

  hexylena

  authored and

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  committed
  fabace7

• Handle data relatively

  

  hexylena

  authored and

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  committed
  7b674da

• working multi-assembly synteny

  

  hexylena

  authored and

  bgruening

  committed
  2095650

• cleanup test data dir

  

  hexylena

  authored and

  bgruening

  committed
  fead3a5

• fix linting

  

  hexylena

  authored and

  bgruening

  committed
  b0e1a67

• new release + fix version

  

  abretaud

  authored and

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  55823fd

• switch back to install from bioconda/biocontainer

  Show description for 7b5bc90
  

  abretaud

  authored and

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  committed
  7b5bc90

• rework default view mechanism

  

  abretaud

  authored and

  bgruening

  committed
  367614a

• fix abs/rel path problems + add cram test

  

  abretaud

  authored and

  bgruening

  committed
  ddb61d3

• fix id collisions

  

  abretaud

  authored and

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  committed
  8b49580

• Support track display choice

  

  abretaud

  authored and

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  committed
  a61f066

• fix bw

  

  abretaud

  authored and

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  d07d27d

• add back tests + udpate todo

  

  abretaud

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  8f250f6

• add jbrowse2 - sorta works a bit - bed and reference only

  

  fubar2

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  b1e0201

• got some things working...bed, gff, bw, ..

  

  fubar2

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  49c627a

• updated bcbio-gff ;0 to 0.7.0 - bcbiogff stopped at 0.6.6

  Show description for 998bb7d
  

  fubar2

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  998bb7d

• more or less working - doesn't open default session although it's in the config :(

  

  fubar2

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  970ae5a

• odd. failing planemo test but runs fine.

  

  fubar2

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  bc8def9

• profile 22.05 breaks with boolean instead of select parameters for conditionals.

  Show description for 2c8bdc6
  

  fubar2

  authored and

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  2c8bdc6

• passes planemo tests and lint now :)

  

  fubar2

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  9c5bb11

• minor cleanup

  

  fubar2

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  0baeadd

• fixed shed.yml :(

  

  fubar2

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  1a09de3

• get rid of some cruft.

  

  fubar2

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  8427e7d

• and more cruft

  

  fubar2

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  57cf121

• Must remove jbrowse-from-dir.xml because it will always fail linting - a test would be needed.

  

  fubar2

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  86db100

• shuffling lines to appease the robot pedants.

  

  fubar2

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  7104451

• robot pedants will always win.

  

  fubar2

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  71a3f8a

• thought this was done

  

  fubar2

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  7a1b33d

• whoopsie - "fixed" the wrong shed.yml :(

  

  fubar2

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  a543771

• evil twins

  

  fubar2

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  1717003

• fix readme.rst - didn't see it :(

  

  fubar2

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  3c8776e

• fix cp

  

  fubar2

  authored and

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  3608161

• cannot get sample vcf to work - header problem reported - tweaking adapter...

  

  fubar2

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  1c08e2c

• flake8 hanging indents fixed...

  

  fubar2

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  792484e

• Update jbrowse2.xml

  bgruening

  committed
  df6c0be

• style formatting

  bgruening

  committed
  ea14dae

• add profile version and fix version command

  bgruening

  committed
  70e6a03

• testing maf

  

  fubar2

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  795eed5

• maf now added - runs and seems to make a track of 3.maf from test-data but need a proper reference/maf test

  

  fubar2

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  e9c9e28

• adding files to branch

  

  fubar2

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  43640dc

• add jbrowse2 - sorta works a bit - bed and reference only

  

  fubar2

  authored and

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  e16f2e6

• got some things working...bed, gff, bw, ..

  

  fubar2

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  a65b57f

• updated bcbio-gff ;0 to 0.7.0 - bcbiogff stopped at 0.6.6

  Show description for 3221a81
  

  fubar2

  authored and

  bgruening

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  3221a81

• more or less working - doesn't open default session although it's in the config :(

  

  fubar2

  authored and

  bgruening

  committed
  b33889c

• odd. failing planemo test but runs fine.

  

  fubar2

  authored and

  bgruening

  committed
  561a145

• profile 22.05 breaks with boolean instead of select parameters for conditionals.

  Show description for a46750d
  

  fubar2

  authored and

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  a46750d

• passes planemo tests and lint now :)

  

  fubar2

  authored and

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  67ea331

• minor cleanup

  

  fubar2

  authored and

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  6db2883

• fixed shed.yml :(

  

  fubar2

  authored and

  bgruening

  committed
  2378b80

• get rid of some cruft.

  

  fubar2

  authored and

  bgruening

  committed
  35c3405

• and more cruft

  

  fubar2

  authored and

  bgruening

  committed
  a5f5f61

• Must remove jbrowse-from-dir.xml because it will always fail linting - a test would be needed.

  

  fubar2

  authored and

  bgruening

  committed
  f548b69

• shuffling lines to appease the robot pedants.

  

  fubar2

  authored and

  bgruening

  committed
  8c6d9cb

• robot pedants will always win.

  

  fubar2

  authored and

  bgruening

  committed
  6999970

• thought this was done

  

  fubar2

  authored and

  bgruening

  committed
  de0cb4a

• whoopsie - "fixed" the wrong shed.yml :(

  

  fubar2

  authored and

  bgruening

  committed
  0e17f9e

• evil twins

  

  fubar2

  authored and

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  committed
  0974d82

• fix readme.rst - didn't see it :(

  

  fubar2

  authored and

  bgruening

  committed
  47b86e9

• fix cp

  

  fubar2

  authored and

  bgruening

  committed
  585ce51

• cannot get sample vcf to work - header problem reported - tweaking adapter...

  

  fubar2

  authored and

  bgruening

  committed
  d827b3a

• flake8 hanging indents fixed...

  

  fubar2

  authored and

  bgruening

  committed
  8459189

• Update jbrowse2.xml

  bgruening

  committed
  3b127fa

• style formatting

  bgruening

  committed
  667cdcc

• add profile version and fix version command

  bgruening

  committed
  4195dd8

• testing maf

  

  fubar2

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  6979205

• maf now added - runs and seems to make a track of 3.maf from test-data but need a proper reference/maf test

  

  fubar2

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  102a059

• flake8 satisfied

  

  fubar2

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  9339f7c

• maf seems to work with some test data - naming of chromosomes and reference are critical for these to work right and

  Show description for c8ceaae
  

  fubar2

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  c8ceaae

• flakery fixed

  

  fubar2

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  539076c

• Update tools/jbrowse2/jbrowse2.xml

  Show description for 114353b
  

  fubar2

  and

  bgruening

  committed
  114353b

• fixed broken test.

  

  fubar2

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  4741c74

• creating branch with hic ready to test

  

  fubar2

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  47c588c

• hic works!

  

  fubar2

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  fad0ca5

• HiC working - the HiC file and the reference now served from a URL so not copied into browser folder

  Show description for 2ea3165
  

  fubar2

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  2ea3165

• odd. passes planemo lint here but fails on ci

  

  fubar2

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  4ccd136

• trying removing profile= from tool to see if planemo lint stops complaining

  

  fubar2

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  ad9face

• nope. not the problem. profile restored.

  

  fubar2

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  651ae01

• fixes to restore maf functionality. Now have blast, maf, bed, bam, gff and vcf test data showing.

  Show description for 3048d69
  

  fubar2

  authored and

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  3048d69

• fix flake8 complaints. Still fails - some CI planemo lint failure?

  

  fubar2

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  8585b32

• fixes for blastxml_to_gapped_gff3.py - works with a PR submitted to bcbio chapmanb/bcbb#141

  Show description for 21b9bf2
  

  fubar2

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  21b9bf2

• remove test_data from JBrowse clone - much smaller archive now.

  

  fubar2

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  c80580c

• fix bogus import for flake8

  

  fubar2

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  b9aab79

• add tabix for bed to see if empty seqtk telo track still causes trouble...

  

  fubar2

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  613c6b3

• datatypes_conf fix

  

  fubar2

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  5353bb0

• added datatypes_conf.xml :( no wonder it didn't work

  

  fubar2

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  7e396e1

• datatypes_conf.xml content is now ignored so remove.

  

  fubar2

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  b273aee

• Changes to allow minimal to use URLs where possible and complete to include everything in the files folder - seems to work...

  

  fubar2

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  3aa5585

• big cleanup.

  Show description for 8e502d6
  

  fubar2

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  8e502d6

• odd. lint failed.

  

  fubar2

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  054e0e4

• fix flake error and lint

  

  fubar2

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  ed3fffc

• local flake differs

  

  fubar2

  authored and

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  e30ffb7

• fix odd problem with spaces in reference names - should be chosen with care.

  

  fubar2

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  a4a8f61

• fixes to deal with different directory structures in conda environments compared to biocontainers.

  Show description for 6b76b3c
  

  fubar2

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  6b76b3c

• passes tests in biocontainers at last.

  Show description for e14101b
  

  fubar2

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  e14101b

• incorporated most of @abretaud's galaxyproject#3997

  Show description for a49b4c9
  

  fubar2

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  a49b4c9

• passes 4 tests but not with biocontainers :(

  Show description for ee6b0e6
  

  fubar2

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  ee6b0e6

• Incorporate all the things missing from abretadeu's galaxyproject#3997

  Show description for f6d562c
  

  fubar2

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  f6d562c

• tests added for vcf and wiggle. Problem with bam - upload always detects binary - how to fix?

  

  fubar2

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  dda7f4a

• passing 6 tests biocontainers too.

  Show description for 2f1fd9f
  

  fubar2

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  2f1fd9f

• rename back to lowercase for consistency and planemo

  

  fubar2

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  3398c39

• update to 1.6.4

  Show description for 7fe902d
  

  abretaud

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  7fe902d

• fixes after rebase

  

  abretaud

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  c735c1d

• rebasing is hard

  

  abretaud

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  d00fc83

• getting harder...

  

  abretaud

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  b3ea5c7

• still stuck. eeesh rebase.

  

  abretaud

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  a3eaeab

• still stuck. infuriating business this.

  

  abretaud

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  7b781c8

• This is mad. Try removing xml and py sources of repeated merge failures :(

  

  abretaud

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  f5c6417

• about to give up

  

  abretaud

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  e120207

• add hic

  

  abretaud

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  fe26bd8

• add default session + general options

  

  abretaud

  authored and

  bgruening

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  641ae94

• update citation

  

  abretaud

  authored and

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  1414917

• Some progress to preconfigure a default session with default tracks and some track rendering options. Half broken/not finished

  

  abretaud

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  f810760

• Final fixes after rebasing to abretaud PR for Helena

  

  fubar2

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  460326e

• some fixes suggested by @hexylena

  

  fubar2

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  1d44168

• Update tools/jbrowse2/jbrowse2.xml

  Show description for f9e19d6
  

  2 peopleauthored and

  bgruening

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  f9e19d6

• Update tools/jbrowse2/macros.xml

  Show description for b51363e
  

  2 peopleauthored and

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  b51363e

• forgot to save...

  

  fubar2

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  29c2957

• fix renamed webserver.py causeing test failure :(

  

  fubar2

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  df7f5cd

• remove noisy logging and printing of progress.

  

  fubar2

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  413ebe2

• add linearpileupdisplay to solve the long loading times for bed tracks with 10s of millions of features from the VGP.

  Show description for 35c6836
  

  fubar2

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  bgruening

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  35c6836

• add styles back

  

  fubar2

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  9c5f8b8

• expand initial view window

  

  fubar2

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  2f2cf7e

• remove names from filenames - they can have tricks in them such as /

  Show description for 495c76d
  

  fubar2

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  495c76d

• updates to current code on EU

  

  fubar2

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  ebb0d97

• Revert "Add bio.tools for abriTAMR (galaxyproject#5561)"

  Show description for 1c0bcd3
  

  fubar2

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  1c0bcd3

• Revert "Revert "Add bio.tools for abriTAMR (galaxyproject#5561)""

  Show description for 9714bd4
  

  fubar2

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  9714bd4

• Revert "updates to current code on EU"

  Show description for 5da583c
  

  fubar2

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  5da583c

• current EU and github code for JBrowse2

  

  fubar2

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  8d73153

• Jbrowse2 tool, still wip

  

  abretaud

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  e993a53

• Run code through black

  

  hexylena

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  29988c2

• Import Ross's changes

  Show description for 40b0b75
  

  fubar2

  authored and

  bgruening

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  40b0b75

• Everything required for assemblies.

  

  hexylena

  authored and

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  be07fca

• The python version is mostly whitespace

  

  hexylena

  authored and

  bgruening

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  88e01c9

• working default behaviour

  

  hexylena

  authored and

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  73ed397

• optional cwd

  

  hexylena

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  ad21772

• Handle data relatively

  

  hexylena

  authored and

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  becd182

• working multi-assembly synteny

  

  hexylena

  authored and

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  158ffa9

• switch back to install from bioconda/biocontainer

  Show description for 897e079
  

  abretaud

  authored and

  bgruening

  committed
  897e079

• rework default view mechanism

  

  abretaud

  authored and

  bgruening

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  525626b

• fix abs/rel path problems + add cram test

  

  abretaud

  authored and

  bgruening

  committed
  1b85fc1

• fix id collisions

  

  abretaud

  authored and

  bgruening

  committed
  25fe825

• Support track display choice

  

  abretaud

  authored and

  bgruening

  committed
  da7dce7

• fix bw

  

  abretaud

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  6636bd4

• lots of challenges from the rebase with the extra layer of repeats for assembly

  

  fubar2

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  dc3b59b

• working with 2 assemblies in a test.

  Show description for 7155f65
  

  fubar2

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  7155f65

• some tests working - still need fixin'

  

  fubar2

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  1f402e0

• tests all passing. removed one with failing menu fussery.

  

  fubar2

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  e7ec48b

• a collection, and 8 phage small samples with hg38 hic URI demonstrations working.

  

  fubar2

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  4ee1e53

• got collection working again...mixed up versions on dev.au - all good now.

  

  fubar2

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  b6efb64

• ensure no spaces in genome uri track names for paf

  

  fubar2

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  e2ffa24

• fix collections again. Now that assemblies are written last..

  

  fubar2

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  6cbda57

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• and more % go.

  

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• remove explicit EDAM in favor of biotools annotation

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• remove autgenJB2 tool, this is now integrated into the main tool

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• revert suite based shed file

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• cleanups

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• fixes for pafs with multiple shared references

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• misc additions

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• Update tools/jbrowse2/autogenJB2.py

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• tweak tests

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• cram not pileup

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• handle default session more gracefully

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• handle more tracks

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• update readme with latest changes from Ross

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• add EDAM and update dependencies+

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• add track_styling_vgp macro

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• simplify pafref handling

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• introduce index_template

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• take over changes from Ross and fix strange bug with contig handling

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• better handling of HiC data

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• improve BAM and CRAM handling

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• improve PAF handling

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• merge in trackset with hash from Anthony

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• remove uglyTestingHack for real

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• use remote (location) test data and adopt tests to include more tracks

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• add more help and creators for real

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• remove deprecated warnings

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• fix Galaxy linting

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• fix SSL errors

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• final cleanup, tests are passing now again

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Commits on May 22, 2024

• remove unused file

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Commits on May 27, 2024

• update JBrowse2

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