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18.09 release#467

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bgruening merged 125 commits intomasterbgruening/docker-galaxy:masterfrom devbgruening/docker-galaxy:devCopy head branch name to clipboardDec 21, 2018

+522-130

Commits

Commits on May 6, 2018

• track dev

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Commits on Aug 5, 2018

• track dev

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• merge

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Commits on Sep 22, 2018

• 18.09 updates

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• new ansible revision

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• use new ansible

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Commits on Sep 23, 2018

• skip test_download_history test

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  0d3a217

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• skip test

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• track 18.09 branch

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Commits on Nov 2, 2018

• use newer python version

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• Update test.sh

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• Update Dockerfile

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Commits on Nov 3, 2018

• skip IE settings

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• Merge branch 'dev' of https://github.com/bgruening/docker-galaxy-stable into dev

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  c4f6aff

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• fix test

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  81ccb16

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• install npm

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  56cdbda

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• enable conda

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  a402c94

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• enable conda

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  84d91b3

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• chown the tool_deps dir

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• tox changes

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• install virtualenv via conda

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• fix conda installation

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  9bf9a5a

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• fix conda installation

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  ebd3ed1

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• install npm

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• install npm

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  4ea5a4f

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• conda

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  a856e1a

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• fixes

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• make image smaller

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• save a few mb

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Commits on Nov 4, 2018

• add deprecation warning

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  190c020

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• use newer conda version

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• Merge branch 'dev' of https://github.com/bgruening/docker-galaxy-stable into dev

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• change permissions

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  2e6c19e

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• use $GALAXY_HOME

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  0d04a9c

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• try something else

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• try something else

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  3193fef

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• try something else

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  70c44e0

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• try something else

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  772b769

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• try something else

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• try something else

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Commits on Nov 6, 2018

• unset variable SUDO_UID, this is needed with newer Conda versions

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• revert last changes

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• add Jelles script

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Commits on Nov 7, 2018

• Fix typo

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  pcm32

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  c175f8d

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• Update docker client version from 17.05 to 17.06.2 and fix download URL

  

  sneumann

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  pcm32

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  272c649

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• Adds script for building containers for k8s for 18.05

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• Makes script more general, includes condor and graphana, makes k8s optional.

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• Adjusts travis and docker compose to work with new building script

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• Improves handling of tags

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• Slurm support

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• Deprecation notice on buildlocal.sh

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• builds condor, k8s, slurm and graphana on travis

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• shows errors of container building phase

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  9459bec

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• Changes tag passing strategy

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  8f850a6

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• Fixes Dockerfile redirection typo

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  3954927

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• Removes additional double quote

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  a02b62b

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• Changes how delim is used with cat

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  b36e8c2

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• Avoids delims and simple echo to file for sourcing

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• Problem was missing if closure.

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• Only last tags should get exported, not entire URIs for travis.

  pcm32

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• Typos for grafana

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• Try compose logs to check status of container before curl call

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• [compose] Pin nodejs to 9.11.1 on init

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• [compose] Removes old adjustments for ubuntu 14.04

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• Don't upgrade pip, 9.0 should be sufficient (should it?)

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• Improves build script from retrievals fro substitutions

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• [compose] Avoid nginx uploading as suggested in gitter

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• [compose] Build client on init

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• use 18.09 version

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• Merge branch 'feature/k8s_container_building_18.09-dev' of https://github.com/bgruening/docker-galaxy-stable into feature/k8s_container_building_18.09-dev

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  c4fb1ac

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• Remove unnecessary copying of client folder.

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Commits on Nov 8, 2018

• Update schema for 18.09

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• install new slurm

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• Merge branch 'feature/k8s_container_building_18.09-dev' of https://github.com/bgruening/docker-galaxy-stable into feature/k8s_container_building_18.09-dev

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Commits on Nov 9, 2018

• Use API based uploads instead of nginx

  pcm32

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• Merge branch 'feature/k8s_container_building_18.09-dev' of https://github.com/bgruening/docker-galaxy-stable into feature/k8s_container_building_18.09-dev

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• enable SGE again

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• Merge branch 'feature/k8s_container_building_18.09-dev' of https://github.com/bgruening/docker-galaxy-stable into feature/k8s_container_building_18.09-dev

  bgruening

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  3b42a88

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• merge layers

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• Merge pull request #462 from bgruening/feature/k8s_container_building_18.09-dev

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  bgruening

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  4a7e7c5

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• remove cruft

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  8e244b6

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Commits on Nov 10, 2018

• install new slurm

  bgruening

  committed
  b6722e4

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• fix syntax

  bgruening

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  cc29851

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Commits on Dec 11, 2018

• update galaxyextras 18.09

  abretaud

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  7d834ec

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• need munge

  abretaud

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• fix slurm install

  abretaud

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  beb8440

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• fix requirements install

  abretaud

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  1be3274

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• try hack for ansible rule

  abretaud

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  2efd525

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• fix for the hack

  abretaud

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  c194c51

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• hack for the hack

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  1481493

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Commits on Dec 12, 2018

• supervisor stuff

  abretaud

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  5bd1ba5

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• no need to mkdir

  abretaud

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  9efc04c

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• slurm startup fix

  abretaud

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  2312f4f

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• For 18.09 uses migration 142, not 144

  abretaud

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  b533b20

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• condor fixes

  abretaud

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  d456e53

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• avoid harmless error message

  abretaud

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  716b859

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• slurm install

  abretaud

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  8f42276

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• fix missing ansible tag

  abretaud

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  57dcde9

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• kube fix?

  abretaud

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• not needed

  abretaud

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Commits on Dec 13, 2018

• move to htcondor-base

  abretaud

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• need 18.09 branch of ansible-galaxy-extras

  abretaud

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  edbef97

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• need nodejs installed (but can't use the ansible task as the galaxy code is not available yet at build time)

  abretaud

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Commits on Dec 14, 2018

• trigger rebuild

  abretaud

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  95a5d7c

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• fix error at startup: this line mounted a not-yet existing file (created later by galaxy-init). It was mounted as an empty dir, so galaxy refused to run. The /usr/bin/startup script will copy the g…

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  abretaud

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• update bioblend testing

  abretaud

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  52f92d4

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• fix bioblend test env

  abretaud

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  e938b86

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Commits on Dec 18, 2018

• fix image tag

  abretaud

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  7e53dc0

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• dump fix

  abretaud

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  5516786

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• reenable client building

  abretaud

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  72866ed

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• fix slurm_singularity test

  abretaud

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  c21cfcc

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• Need to delay setting of GALAXY_CONFIG_TOOL_CONFIG_FILE

  abretaud

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• create needed dirs/files for condor

  abretaud

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  27ee4ab

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• update tag

  abretaud

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  2c0be52

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• latest kubernetes needs go >=1.11.1

  abretaud

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  40b74ac

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• fix path problem (not sure if sudo is really needed)

  abretaud

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  7beba07

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• longer timeout

  abretaud

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• Longer timeout

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Commits on Dec 19, 2018

• fix ignored BIOBLEND_TEST_JOB_TIMEOUT

  abretaud

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  1cf3215

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• wait more!?

  abretaud

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• update kompose

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Commits on Dec 21, 2018

• Merge pull request #464 from abretaud/1804

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  bgruening

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• shift deprecation warning to 19.05 as I failed to release this version in time

  bgruening

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• I don't feel good to install beta versions in stable releases, even if it is 10times faster

  bgruening

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• add news entry

  bgruening

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