Code

Jbrowse2 tool#3997

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abretaud wants to merge 45 commits intogalaxyproject:maingalaxyproject/tools-iuc:mainfrom abretaud:jbrowse2abretaud/tools-iuc:jbrowse2Copy head branch name to clipboard

+18,536

Commits

Commits on Mar 6, 2023

• Jbrowse2 tool, still wip

  abretaud

  committed
  99dde37

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• fix

  abretaud

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  4503b39

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• update to 1.6.4

  abretaud

  committed
  515a3f4

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• remove the standalone option, not very useful for jbrowse2

  abretaud

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  4f93c75

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• genetic code not available yet

  abretaud

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  a525386

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• upate todos

  abretaud

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  fe743c4

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• sparql

  abretaud

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  912c150

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• sparql

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  cc40f6e

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• add synteny track

  abretaud

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  6c40116

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• add cram

  abretaud

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  78da74e

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• add vcf_bgzip

  abretaud

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  f691dc5

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• auto conversion does the job

  abretaud

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  c1f8ca4

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• add hic

  abretaud

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  587c473

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• Fix xml polluted with SafeStringWrapper

  abretaud

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  4135153

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• log/fix track pocessing

  abretaud

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  f17a138

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• Fix updating existing jbrowse dataset

  abretaud

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  ad0d69a

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• some progress on synteny

  abretaud

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  6fb4d38

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• add default session + general options

  abretaud

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  d7c446e

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• update citation

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  0b5b576

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• lint

  abretaud

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  27f448f

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

  abretaud

  committed
  8bc1049

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• update to 1.6.5

  abretaud

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  6838753

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• update to 1.6.6

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  0a0d29f

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• typo

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  b8e7213

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• be prepared for other synteny formats

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  b34fda0

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• progress on default track display

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  015732c

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• update/spaces

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  ed79f43

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Commits on Mar 7, 2023

• add back tests + udpate todo

  abretaud

  committed
  a462ff9

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Commits on Jan 26, 2024

• Run code through black

  hexylena

  committed
  ce6f6d6

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• Import Ross's changes

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  fubar2

  authored and

  hexylena

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• Everything required for assemblies.

  hexylena

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  2005e27

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• The python version is mostly whitespace

  hexylena

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  692d2f0

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• working default behaviour

  hexylena

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  dad485e

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• optional cwd

  hexylena

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  118a5e2

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• Handle data relatively

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  6739631

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Commits on Jan 29, 2024

• working multi-assembly synteny

  hexylena

  committed
  7989040

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• cleanup test data dir

  hexylena

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  cf12f89

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Commits on Feb 15, 2024

• fix linting

  hexylena

  committed
  3c51f3b

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Commits on Feb 23, 2024

• new release + fix version

  abretaud

  committed
  4dbfdba

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Commits on Feb 27, 2024

• switch back to install from bioconda/biocontainer

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  abretaud

  committed
  4561e21

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Commits on Mar 6, 2024

• rework default view mechanism

  abretaud

  committed
  c64d0f0

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• fix abs/rel path problems + add cram test

  abretaud

  committed
  987aba2

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Commits on Mar 12, 2024

• fix id collisions

  abretaud

  committed
  e6e3ca2

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• Support track display choice

  abretaud

  committed
  95384f5

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• fix bw

  abretaud

  committed
  5ebfe0b

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