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Jbrowse2#5695

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fubar2 wants to merge 89 commits intogalaxyproject:maingalaxyproject/tools-iuc:mainfrom fubar2:jbrowse2fubar2/tools-iuc:jbrowse2Copy head branch name to clipboard

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Commits on Dec 24, 2023

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

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  15a045a

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• Merge branch 'galaxyproject:main' into jbrowse2

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

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• Merge branch 'jbrowse2' of github.com:fubar2/tools-iuc into jbrowse2

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Commits on Dec 25, 2023

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

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Commits on Dec 26, 2023

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

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• odd. failing planemo test but runs fine.

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Commits on Dec 27, 2023

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

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• passes planemo tests and lint now :)

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• minor cleanup

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• fixed shed.yml :(

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• get rid of some cruft.

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• and more cruft

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

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• shuffling lines to appease the robot pedants.

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• robot pedants will always win.

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• thought this was done

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

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• evil twins

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• fix readme.rst - didn't see it :(

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• fix cp

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

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• Update jbrowse2.xml

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• style formatting

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• add profile version and fix version command

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  9bf5779

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• flake8 hanging indents fixed...

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• Merge branch 'jbrowse2' of github.com:fubar2/tools-iuc into jbrowse2

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Commits on Dec 28, 2023

• testing maf

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

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• adding files to branch

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

  fubar2

  committed
  0ebd0ce

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

  fubar2

  committed
  94c4b9a

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

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

  fubar2

  committed
  bd3dc60

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• odd. failing planemo test but runs fine.

  fubar2

  committed
  e30d3a1

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

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• passes planemo tests and lint now :)

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  committed
  c880c19

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• minor cleanup

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  6ade364

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• fixed shed.yml :(

  fubar2

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  86942c0

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• get rid of some cruft.

  fubar2

  committed
  7f5bc3a

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• and more cruft

  fubar2

  committed
  136ac1e

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

  fubar2

  committed
  5f43e3f

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• shuffling lines to appease the robot pedants.

  fubar2

  committed
  6fbfae0

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• robot pedants will always win.

  fubar2

  committed
  b8c49dc

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• thought this was done

  fubar2

  committed
  adc6142

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

  fubar2

  committed
  62eb033

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• evil twins

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  7ec0460

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• fix readme.rst - didn't see it :(

  fubar2

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  8a7f103

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• fix cp

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  9b92344

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

  fubar2

  committed
  5f4d47d

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• flake8 hanging indents fixed...

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  committed
  d2b8255

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• Update jbrowse2.xml

  

  bgruening

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  fubar2

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  ae792f2

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• style formatting

  

  bgruening

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  fubar2

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  f89a898

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• add profile version and fix version command

  

  bgruening

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  fubar2

  committed
  2d7445c

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• testing maf

  fubar2

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  5a899ea

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

  fubar2

  committed
  0e05b8c

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• adding files to branch

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• Merge branch 'jb2maf' of github.com:fubar2/tools-iuc into jb2maf

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• flake8 satisfied

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Commits on Dec 29, 2023

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

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• flakery fixed

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• Update tools/jbrowse2/jbrowse2.xml

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  and

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• fixed broken test.

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  d7ce5b0

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Commits on Dec 30, 2023

• creating branch with hic ready to test

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Commits on Jan 2, 2024

• hic works!

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

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• odd. passes planemo lint here but fails on ci

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

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• nope. not the problem. profile restored.

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

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

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Commits on Jan 3, 2024

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

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

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  8fc7579

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• fix bogus import for flake8

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

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• datatypes_conf fix

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• Merge branch 'galaxyproject:main' into jbrowse2

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

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• Merge branch 'jbrowse2' of github.com:fubar2/tools-iuc into jbrowse2

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• datatypes_conf.xml content is now ignored so remove.

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Commits on Jan 4, 2024

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

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Commits on Jan 5, 2024

• big cleanup.

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• odd. lint failed.

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  83bcdf8

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• fix flake error and lint

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  9455446

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• local flake differs

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  92edea2

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

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

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• passes tests in biocontainers at last.

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Commits on Jan 6, 2024

• Merge branch 'galaxyproject:main' into jbrowse2

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