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Add support for running IRIDA#589

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pvanheus wants to merge 36 commits intobgruening:masterbgruening/docker-galaxy:masterfrom combat-sars-cov-2:irida_supportcombat-sars-cov-2/workbench:irida_supportCopy head branch name to clipboard

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Commits

Commits on Nov 15, 2021

• Add support for running IRIDA with Galaxy

  pvanheus

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  29741aa

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• Add scripts for configuring IRIDA (WIP)

  pvanheus

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  44d61d7

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Commits on Nov 18, 2021

• use newer Singularity release

  bgruening

  authored
  27e5611

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• try different link

  bgruening

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Commits on Mar 17, 2022

• Update IRIDA to version 22.04.1

  pvanheus

  committed
  f126e0f

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• Update login page to work with IRIDA 22

  pvanheus

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Commits on May 22, 2022

• Add notes to README

  pvanheus

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  16cd557

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• Update IRIDA to 22.03.1

  pvanheus

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  1c2e2cf

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• Update to 0.1.8 of the nanopore workflow

  pvanheus

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• Set auto_install to False

  pvanheus

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  10bdddb

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• Add comment about conda install

  pvanheus

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  a68e838

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• Removed packaged versions of pipeline jars

  pvanheus

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  e81046f

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• Add Africa CDC logo to branding

  pvanheus

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  620522a

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• Fix Africa CDC logo

  pvanheus

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  4efc070

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• Add margin back into top logo row

  pvanheus

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  e231a40

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• Change Africa CDC logo

  pvanheus

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  14f9a4f

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• Remove galaxy_tools.yml, this will be build on demand

  pvanheus

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  70cec58

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• Add config for running primer scheme DM

  pvanheus

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  34bb8e2

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• Force dependency_resolvers_conf.xml to be empty

  pvanheus

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  fec61a7

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• Ignore galaxy_tools.yml

  pvanheus

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  f8e36cd

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• Set install_resolver_dependencies to False

  pvanheus

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  b52ecfe

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• Correct tool id in primer bed DM config

  pvanheus

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  5a08991

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• Update to latest primer scheme DM

  pvanheus

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  551a100

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Commits on May 24, 2022

• Update Illumina workflow to version 0.1.11

  pvanheus

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Commits on Jun 3, 2022

• set HOME to /home/galaxy

  pvanheus

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  d76f0e2

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• Upgrade IRIDA to 22.05.1

  pvanheus

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  8670a83

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• Fix comment

  pvanheus

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  d690bef

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• Add SSL support for IRIDA

  pvanheus

  committed
  7a31f5f

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• Explain how to enable SSL for IRIDA

  pvanheus

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  20e5cfc

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• Add port 443 for SSL

  pvanheus

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  3482a95

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• Add TODO

  pvanheus

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  1b52ef3

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Commits on Jun 4, 2022

• Remove Illumina plugin jar

  pvanheus

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Commits on Oct 6, 2022

• Update IRIDA to version 22.05.5

  pvanheus

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  b57f621

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• Simplify gosu install, set tomcat to explicitely use jdk11

  pvanheus

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  989f65e

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Commits on Oct 11, 2022

• Update to latest workflows

  pvanheus

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  9ead030

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• Remove tmp directory with old workflows

  pvanheus

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