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I don't understand, 1.16.6 doesn't appear in Gemfile.lock https://dev.arvados.org/projects/arvados/repository/revisions/1.4-dev/entry/apps/workbench/Gemfile.lock
now I'm wondering if the package building does something strange
uh,
arvados-workbench_1.4.3-1_amd64.deb is not the same as arvados-workbench-server_1.4.3-1_amd64.deb ?
It is 1.16.6 for api
bundler is supposed to solve problems but lately it has mostly been causing them
@dantetwc what happens if you do
gem install bundler --version 2.0.2 before you try to install a Rails package
produce same error
@tetron Nope, I am not working with Antonio
ok, so, I'm glad you found a workaround
I am working on the 1.5 release and am hoping to start building a release candidate and testing next week
I should mention if your company is looking for professional support or feature development to contact info@curii.com
Wanted to integrated with other tools of our company and automatically start a task by using API
@dantetwc This is quite old and I'm not sure if it still works. @tetron maybe something for the cookbook? Any improvements are welcome
@dantetwc also, there is https://github.com/common-workflow-language/workflow-service which implements the GA4GH Workflow Execution Service API using Arvados
@dantetwc https://bundler.io/blog/2019/05/14/solutions-for-cant-find-gem-bundler-with-executable-bundle.html there's a note about needing to update
gem along with bundler and that bundler 2.0 has a new version switching behavior
bundler 2.0 seems to require RubyGems 3.0
Hi @tetron,
When I bring up workbench, I am getting an error that makes me think my application.yml file isn't recognized, although I've confirmed that a symlink exists at /var/www/arvados-workbench/current/config/application.yml. I'm having difficulty figuring out what's failing in the load_config.rb. Does you know off hand of any gotchas I should look out for, or have you seen this error message before?
2020-01-21T21:16:00.4286668Z App 1315 output: The following configuration settings must be specified in
2020-01-21T21:16:00.428671167Z App 1315 output: config/application.yml:
2020-01-21T21:16:00.428674283Z App 1315 output: * arvados_login_base
2020-01-21T21:16:00.42867761Z App 1315 output: * arvados_v1_base
2020-01-21T21:16:00.42868134Z App 1315 output: * arvados_insecure_https
2020-01-21T21:16:00.428721642Z App 1315 output: * secret_token
@Jacoberts I believe it makes a symlink from /var/www/arvados-workbench/current/config/application.yml to /etc/arvados/api/application.yml (or similar)
those keys need to be in the 'common' or 'production' section of the yml file
Dante … user cwl bwa-mem arvados-cwl-runner --create-workflow bwa-mem.cwl bwa-mem-template.yml master
2020-01-22 17:47:08 cwltool INFO: /Users/Dante/Library/Python/2.7/bin/arvados-cwl-runner 1.4.2, arvados-python-client 1.4.2, cwltool 1.0.20181217162649
2020-01-22 17:47:08 cwltool INFO: Resolved 'bwa-mem.cwl' to 'file:///Users/Dante/Downloads/arvados/doc/user/cwl/bwa-mem/bwa-mem.cwl'
2020-01-22 17:47:09 arvados.arv-run INFO: Using empty collection d41d8cd98f00b204e9800998ecf8427e+0
2020-01-22 17:47:09 arvados.arv-run INFO: Using empty collection d41d8cd98f00b204e9800998ecf8427e+0
2020-01-22 17:47:09 arvados.arv-run INFO: Using empty collection d41d8cd98f00b204e9800998ecf8427e+0
arv01-7fd4e-r2vhghpwkybtkn5
2020-01-22 17:47:09 cwltool INFO: Final process status is success
Dante … user cwl bwa-mem arvados-cwl-runner --debug arv01-7fd4e-r2vhghpwkybtkn5 master
2020-01-22 17:47:22 cwltool INFO: /Users/Dante/Library/Python/2.7/bin/arvados-cwl-runner 1.4.2, arvados-python-client 1.4.2, cwltool 1.0.20181217162649
2020-01-22 17:47:22 cwltool INFO: Resolved 'arv01-7fd4e-r2vhghpwkybtkn5' to 'arvwf:arv01-7fd4e-r2vhghpwkybtkn5#main'
2020-01-22 17:47:22 cwltool ERROR: I'm sorry, I couldn't load this CWL file.
The error was:
Traceback (most recent call last):
File "/Users/Dante/Library/Python/2.7/lib/python/site-packages/cwltool/main.py", line 646, in main
fetcher_constructor=loadingContext.fetcher_constructor)
File "/Users/Dante/Library/Python/2.7/lib/python/site-packages/cwltool/load_tool.py", line 117, in fetch_document
workflowobj = document_loader.fetch(fileuri)
File "/Users/Dante/Library/Python/2.7/lib/python/site-packages/schema_salad/ref_resolver.py", line 961, in fetch
result = yaml.round_trip_load(textIO, preserve_quotes=True)
File "/usr/local/Cellar/python@2/2.7.17_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ruamel/yaml/main.py", line 144, in round_trip_load
return load(stream, RoundTripLoader, version, preserve_quotes=preserve_quotes)
File "/usr/local/Cellar/python@2/2.7.17_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ruamel/yaml/main.py", line 95, in load
return loader._constructor.get_single_data()
File "/usr/local/Cellar/python@2/2.7.17_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ruamel/yaml/constructor.py", line 86, in get_single_data
node = self.composer.get_single_node()
File "/usr/local/Cellar/python@2/2.7.17_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ruamel/yaml/composer.py", line 79, in get_single_node
event.start_mark)
ComposerError: expected a single document in the stream
in "arvwf:arv01-7fd4e-r2vhghpwkybtkn5", line 1, column 1
but found another document
in "arvwf:arv01-7fd4e-r2vhghpwkybtkn5", line 128, column 1
Dante … user cwl bwa-mem
trying to create a workflow following the guide here https://doc.arvados.org/master/user/tutorials/writing-cwl-workflow.html
but it didn't work
any insight?
@dantetwc I'll have to try it later and see what result I get
Looks like you are running it on OS X?
http://rpm.arvados.org/CentOS/2/os/x86_64/repodata/repomd.xml: [Errno 14] HTTP Error 404 - Not Found
Trying other mirror.
Trying other mirror.
Nevermind I found the issue