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Target Miniconda3 when installing Conda. #3419

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merged 2 commits into from Jan 13, 2017

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@jmchilton
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commented Jan 13, 2017

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else:
url = "https://repo.continuum.io/miniconda/Miniconda2-4.0.5-Linux-x86_64.sh"
url = "https://repo.continuum.io/miniconda/Miniconda3-4.0.5-Linux-x86_64.sh"

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@mvdbeek

mvdbeek Jan 13, 2017

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Shouldn't we go to the latest stable MIniconda ? (4.2.12, as far as I can tell)

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@jmchilton

jmchilton Jan 13, 2017

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Done.

@@ -358,6 +358,7 @@ def install_conda(conda_context=None):
fix_version_cmd = "%s install -y -q conda=%s " % (os.path.join(conda_context.conda_prefix, 'bin/conda'), CONDA_VERSION)
full_command = "%s && %s && %s" % (download_cmd, install_cmd, fix_version_cmd)
try:
log.info("Installing Conda this may take several minutes.")

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@nsoranzo

nsoranzo Jan 13, 2017

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Add a comma after Conda?

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@mvdbeek

mvdbeek Jan 13, 2017

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and maybe "To skip automatic installation of conda, set conda_auto_install = False in galaxy.ini" ?

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@jmchilton

jmchilton Jan 13, 2017

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I made the first change. I'd rather not be so specific here because it is library code. That message for Galaxy specifically would have to go somewhere else or an extension point would need to be introduced to allow this.

jmchilton added some commits Jan 13, 2017

Switch to Miniconda3.
It is the platformed used by bioconda for testing and will be supported longer than the older Python 2 variant. This shouldn't require Python 3 be installed on the host running Galaxy.

@jmchilton jmchilton force-pushed the jmchilton:conda_tweaks branch from 46a7e7d to d66d3a1 Jan 13, 2017

@jxtx

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commented Jan 13, 2017

This is probably discussed somewhere else, but, why?

@jmchilton

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commented Jan 13, 2017

@jxtx

  • It will be supported for longer than miniconda 2 according to @bgruening.
  • It is the platform used for testing bioconda - so we can be more confident in the bioconda testing translating to successful Galaxy usage.

@martenson martenson merged commit 1f9812b into galaxyproject:dev Jan 13, 2017

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@bgruening

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commented Jan 13, 2017

@jxtx miniconda indicates the python version is ships in the root environment. I doubt they will support it after 2019. So we thought before we make conda default, we go with miniconda3 (python3 in root) to be more future proof.

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commented Jan 13, 2017

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