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fix bootstrap.py with proxy #15834

Merged
merged 2 commits into from
Jun 14, 2019
Merged

fix bootstrap.py with proxy #15834

merged 2 commits into from
Jun 14, 2019

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pirovc
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@pirovc pirovc commented Jun 13, 2019

Bioconda requires reviews prior to merging pull-requests (PRs). To facilitate this, once your PR is passing tests and ready to be merged, please add the please review & merge label so other members of the bioconda community can have a look at your PR and either make suggestions or merge it. Note that if you are not already a member of the bioconda project (meaning that you can't add this label), please ping @bioconda/core so that your PR can be reviewed and merged (please note if you'd like to be added to the bioconda project). Please see #15332 for more details.

  • I have read the guidelines for bioconda recipes.
  • This PR adds a new recipe.
  • AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
  • This PR updates an existing recipe.
  • This PR does something else (explain below).

Under a machine with a proxy configured the script bootstrap.py was failing with the following error:

$ ./bootstrap.py /tmp/miniconda
fatal: unable to access 'https://github.com/bioconda/bioconda-recipes.git/': Failed to connect to github.com port 443: Connection refused
Traceback (most recent call last):
  File "bootstrap.py", line 110, in <module>
    sp.check_call(['.circleci/setup.sh'], env=env)
  File "/usr/lib/python3.5/subprocess.py", line 271, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['.circleci/setup.sh']' returned non-zero exit status 128

This PR should fix it by passing the https_proxy variable to the .circleci/setup.sh call.

@bioconda/core please check

@epruesse
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Does this fix the problem for you? Does the whole thing work?
I've messed with some of the docker stuff recently, and there was https_proxy specific code in there. If you could try whether bioconda build --docker (and --mulled) work, that would be very much appreciated.

@biocondabot
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biocondabot bot commented Jun 13, 2019

No artifacts found on recent CircleCI builds.

@epruesse epruesse merged commit 1b76732 into master Jun 14, 2019
@pirovc pirovc deleted the bugfix/bootstrap-with-proxy branch June 15, 2019 11:30
kpalin pushed a commit to kpalin/bioconda-recipes that referenced this pull request Aug 7, 2019
* pass env. variable https_proxy to the setup.sh call

* allow HTTPS_PROXY as well
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2 participants