Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix virtualenv activation for some scripts #4616

Merged
merged 1 commit into from Sep 15, 2017

Conversation

Projects
None yet
3 participants
@nsoranzo
Copy link
Member

commented Sep 14, 2017

In particular add virtualenv activation to extract_dataset_parts.sh to fix the following error when running tools which use <parallelism>:

Fatal error:
/tmp/tmpOoQ01k/job_working_directory/000/12/task_0:
Traceback (most recent call last):
File "./scripts/extract_dataset_part.py", line 17, in <module>
import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module>
from six import string_types
ModuleNotFoundError: No module named 'six'
Fix virtualenv activation for some scripts
In particular add virtualenv activation to extract_dataset_parts.sh
to fix the following error when running tools which use
`<parallelism>`:
```
Fatal error:
/tmp/tmpOoQ01k/job_working_directory/000/12/task_0:
Traceback (most recent call last):
File "./scripts/extract_dataset_part.py", line 17, in <module>
import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module>
from six import string_types
ModuleNotFoundError: No module named 'six'
```
@jmchilton

This comment has been minimized.

Copy link
Member

commented Sep 14, 2017

@mvdbeek Are these integration test failures unrelated?

@mvdbeek

This comment has been minimized.

Copy link
Member

commented Sep 14, 2017

Looks like a network issue:

raceback (most recent call last):
      File "/tmp/tmpH_mnCR/conda/lib/python3.5/site-packages/conda/fetch.py", line 395, in download
        resp.raise_for_status()
      File "/tmp/tmpH_mnCR/conda/lib/python3.5/site-packages/requests/models.py", line 862, in raise_for_status
        raise HTTPError(http_error_msg, response=self)
    requests.exceptions.HTTPError: 503 Server Error: Slow Down for url:

Most likely unrelated, I'd say.

@mvdbeek mvdbeek merged commit 90eed10 into galaxyproject:dev Sep 15, 2017

5 of 6 checks passed

continuous-integration/travis-ci/pr The Travis CI build is in progress
Details
api test Build finished. 292 tests run, 4 skipped, 0 failed.
Details
framework test Build finished. 161 tests run, 0 skipped, 0 failed.
Details
integration test Build finished. 45 tests run, 0 skipped, 0 failed.
Details
lgtm analysis: JavaScript No alert changes
Details
toolshed test Build finished. 579 tests run, 0 skipped, 0 failed.
Details
@mvdbeek

This comment has been minimized.

Copy link
Member

commented Sep 15, 2017

Thanks @nsoranzo !

@nsoranzo nsoranzo deleted the nsoranzo:fix_scripts branch Sep 15, 2017

nsoranzo referenced this pull request in peterjc/galaxy_blast Sep 15, 2017

dannon added a commit that referenced this pull request Sep 15, 2017

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.