Galaxy upgrade error

1

Hello

I wanted to upgrade Galaxy but it shows :
error: Your local changes to the following files would be overwritten by checkout:
…
Aborting

If I try to start it also it shows :
./scripts/common_startup.sh: line 271: 21034 Aborted yarn install --network-timeout 300000 --check-files
ERROR: Galaxy client dependency installation failed.

Any assistance Please ???

THANKS

1 Like
2

This looks like two errors – let’s separate them.

First, do you have local changes that you know of? What is the output of git status, what exactly were you trying to checkout, and from what branch/state?

And, for the second, is there any additional error output at all? What if you try a make client from the galaxy root directory?

1 Like
3

Hi Dannon,

git status output gives:
fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

For the output of sh run.sh :
The Galaxy client is out of date and will be built now.
yarn install v1.17.3
[1/4] Resolving packages…
success Already up-to-date.
warning Your current version of Yarn is out of date. The latest version is “1.22.5”, while you’re on “1.17.3”.
info To upgrade, run the following command:
$ curl --compressed -o- -L https://yarnpkg.com/install.sh | bash
Done in 4.67s.
./scripts/common_startup.sh: line 271: 505 Aborted yarn install --network-timeout 300000 --check-files
ERROR: Galaxy client dependency installation failed. See ./client/README.md for more information, including how to get help.

4

Well, let’s take the first problem first. How did you install this Galaxy if it isn’t git based?

1 Like
5

It was from 2 years ago and I really forgot

But I think , git clone …git then moved the folder to another directory !

6

root@tesla:/usr/local/galaxy# git fetch origin && git checkout release_20.05 && git pull --ff-only origin release_20.05
remote: Enumerating objects: 2173, done.
remote: Counting objects: 100% (2173/2173), done.
remote: Compressing objects: 100% (76/76), done.
remote: Total 2910 (delta 2119), reused 2149 (delta 2095), pack-reused 737
Receiving objects: 100% (2910/2910), 3.77 MiB | 267.00 KiB/s, done.
Resolving deltas: 100% (2281/2281), completed with 1006 local objects.
From https://github.com/galaxyproject/galaxy
01f2a7933d…bc68f785f9 20.09_release_notes -> origin/20.09_release_notes

  • e2c7d623cd…c6e8889a7b anvil -> origin/anvil (forced update)
    1cc3d5b178…b7e1a8573d dev -> origin/dev
    0c462a46b9…e3c5df3b5f master -> origin/master
    acfe5624b6…999a2c3f4b release_20.01 -> origin/release_20.01
    bcae7d41c9…e3c5df3b5f release_20.05 -> origin/release_20.05
    97cd907cd3…acf949d341 release_20.09 -> origin/release_20.09
  • 4f56a029c6…04882252b3 usegalaxy -> origin/usegalaxy (forced update)
  • [new tag] galaxy-app-20.9.0 -> galaxy-app-20.9.0
  • [new tag] galaxy-auth-20.9.0 -> galaxy-auth-20.9.0
  • [new tag] galaxy-data-20.9.0 -> galaxy-data-20.9.0
  • [new tag] galaxy-job-execution-20.9.0 -> galaxy-job-execution-20.9.0
  • [new tag] galaxy-job-metrics-20.9.0 -> galaxy-job-metrics-20.9.0
  • [new tag] galaxy-objectstore-20.9.0 -> galaxy-objectstore-20.9.0
  • [new tag] galaxy-selenium-20.9.0 -> galaxy-selenium-20.9.0
  • [new tag] galaxy-test-api-20.9.0 -> galaxy-test-api-20.9.0
  • [new tag] galaxy-test-base-20.9.0 -> galaxy-test-base-20.9.0
  • [new tag] galaxy-test-driver-20.9.0 -> galaxy-test-driver-20.9.0
  • [new tag] galaxy-test-selenium-20.9.0 -> galaxy-test-selenium-20.9.0
  • [new tag] galaxy-tool-util-20.9.0 -> galaxy-tool-util-20.9.0
  • [new tag] galaxy-util-20.9.0 -> galaxy-util-20.9.0
  • [new tag] galaxy-web-framework-20.9.0 -> galaxy-web-framework-20.9.0
    error: Your local changes to the following files would be overwritten by checkout:
    .ci/flake8_blacklist.txt
    .ci/jenkins/selenium-compose/Dockerfile
    .circleci/config.yml
    .gitignore
    .travis.yml
    CONTRIBUTING.md
    CONTRIBUTORS.md
    Makefile
    README.rst
    client/.eslintrc.js
    client/.node_version
    client/README.md
    client/galaxy/docs/bootstrap.md
    client/galaxy/docs/galaxy-buttons.md
    client/galaxy/images/light_gray_grid.gif
    client/galaxy/scripts/admin.toolshed.js
    client/galaxy/scripts/app/galaxy.js
    client/galaxy/scripts/app/monitor.js
    client/galaxy/scripts/bundleEntries.js
    client/galaxy/scripts/components/Alert.vue
    client/galaxy/scripts/components/Citations.vue
    client/galaxy/scripts/components/DataDialog/DataDialog.test.js
    client/galaxy/scripts/components/DataDialog/DataDialog.vue
    client/galaxy/scripts/components/DataDialog/DataDialogSearch.vue
    client/galaxy/scripts/components/DataDialog/DataDialogTable.vue
    client/galaxy/scripts/components/DataDialog/model.js
    client/galaxy/scripts/components/DataDialog/services.js
    client/galaxy/scripts/components/DisplayStructured.vue
    client/galaxy/scripts/components/GalaxyLoader.vue
    client/galaxy/scripts/components/HistoryImport.vue
    client/galaxy/scripts/components/HistoryView.vue
    client/galaxy/scripts/components/Masthead/index.vue
    client/galaxy/scripts/components/Masthead/initMasthead.js
    client/galaxy/scripts/components/Message.vue
    client/galaxy/scripts/components/Nametags/Nametag.vue
    client/galaxy/scripts/components/Nametags/Nametags.vue
    client/galaxy/scripts/components/PluginList.vue
    client/galaxy/scripts/components/RuleCollectionBuilder.vue
    client/galaxy/scripts/components/RulesDisplay.vue
    client/galaxy/scripts/components/Select2.js
    client/galaxy/scripts/components/Sharing.vue
    client/galaxy/scripts/components/Tags/StatelessTags.test.js
    client/galaxy/scripts/components/Tags/StatelessTags.vue
    client/galaxy/scripts/components/Tags/Tags.test.js
    client/galaxy/scripts/components/Tags/Tags.vue
    client/galaxy/scripts/components/Tags/model.js
    client/galaxy/scripts/components/Tags/mounts.js
    client/galaxy/scripts/components/Tags/tagService.js
    client/galaxy/scripts/components/Tags/tagService.test.js
    client/galaxy/scripts/components/WorkflowImport.vue
    client/galaxy/scripts/components/admin/AdminServices.js
    client/galaxy/scripts/components/admin/BaseGrid.vue
    client/galaxy/scripts/components/admin/DataManager/DataManager.vue
    client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue
    client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
    client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue
    client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
    client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue
    client/galaxy/scripts/components/admin/DataManagerGrid.vue
    client/galaxy/scripts/components/admin/DataTables.vue
    client/galaxy/scripts/components/admin/DataTablesGrid.vue
    client/galaxy/scripts/components/admin/DataTypes.vue
    client/galaxy/scripts/components/admin/DisplayApplications.vue
    client/galaxy/scripts/components/admin/ErrorStack.vue
    client/galaxy/scripts/components/login/Index.vue
    client/galaxy/scripts/components/login/Login.vue
    client/galaxy/scripts/components/login/Password.vue
    client/galaxy/scripts/components/login/Register.vue
    client/galaxy/scripts/entry/admin/AdminRouter.js
    client/galaxy/scripts/entry/admin/index.js
    client/galaxy/scripts/entry/analysis/AnalysisRouter.js
    client/galaxy/scripts/entry/analysis/index.js
    client/galaxy/scripts/entry/login/index.js
    client/galaxy/scripts/entry/panels/admin-panel.js
    client/galaxy/scripts/entry/panels/history-panel.js
    client/galaxy/scripts/entry/panels/tool-panel.js
    client/galaxy/scripts/galaxy.interactive_environments.js
    client/galaxy/scripts/galaxy.library.js
    client/galaxy/scripts/galaxy.pages.js
    client/galaxy/scripts/i18n.js
    client/galaxy/scripts/layout/communication-server-view.js
    client/galaxy/scripts/layout/data.js
    client/galaxy/scripts/layout/masthead.js
    client/galaxy/scripts/layout/menu.js
    client/galaxy/scri
    Aborting
1 Like
7

ping @dannon

Related Q&A is linked back for context (starting with a new checkout >> Galaxy upgrade error