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Change Conda channel order #3237

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merged 6 commits into from
Dec 12, 2016
Merged

Change Conda channel order #3237

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8519e12
change conda channel order
bgruening Dec 1, 2016
1f221aa
change channel order
bgruening Dec 1, 2016
0c91f65
Change channel order in documentation
bgruening Dec 1, 2016
8a80b2d
change order in galaxy.ini
bgruening Dec 12, 2016
3d49265
change oder in docs
bgruening Dec 12, 2016
f693643
change channel order in conda.py
bgruening Dec 12, 2016
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3 changes: 2 additions & 1 deletion config/galaxy.ini.sample
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Expand Up @@ -203,7 +203,8 @@ paste.app_factory = galaxy.web.buildapp:app_factory
# Pass debug flag to conda commands.
#conda_debug = False
# conda channels to enable by default (http://conda.pydata.org/docs/custom-channels.html)
#conda_ensure_channels = conda-forge,r,bioconda,iuc
# the recommended channel order is the one from BioConda (https://github.com/bioconda/bioconda-recipes/blob/master/config.yml#L8)
#conda_ensure_channels = bioconda,r,defaults,conda-forge,iuc
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Isn't iuc channel supposed to be used (also) to fix problems with packages in other channels? If we put it last, it's not very useful. It should probably be first, no?

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This really depends on what we want to use this channel for. My Intension was to put in old recipes, that are outdated and we don't want to have in bioconda, or some ugly hacks (but for new recipes). Not replacing/overwriting recipes from other channels.

Up for discussion I suppose.

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If iuc is only for old recipes, its position shouldn't matter, but if we are ever going to need to use it for some "ugly hack" it needs to be first.

Has any one else opinions here?

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I am +1 on having a channel we directly control as the first entry here. Can we create a new one for this purposes?

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I understand the desire to have like an IUC override channel for hacks. I don't think we need it yet though and it probably shouldn't hold up this PR. Can we create a low priority issue for that and continue with this correction?

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@martenson Do you mean an additional one? I think one "Galaxy" channel should be enough and iuc is mostly unused.

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@jmchilton @bgruening I don't think there is a rush to merge this or the need to backport it since channel order in Conda 3.19.3 matters only if 2 packages have the same version and build numbers. This changed in Conda 4.1.0, see http://conda.pydata.org/docs/channels.html

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@martenson martenson Dec 6, 2016 •
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@nsoranzo Does putting iuc first have any unwanted effects?
@jmchilton this targets 17.01 - no rush, right?

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@martenson iuc channel seems to have 3 packages, all in a version different from what's available in bioconda.

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I honestly don't know. You guys decide.

# Set to True to instruct Galaxy to look for and install missing tool
# dependencies before each job runs.
#conda_auto_install = False
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2 changes: 1 addition & 1 deletion doc/source/admin/dependency_resolvers.rst
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Expand Up @@ -182,7 +182,7 @@ debug
ensure_channels
conda channels to enable by default. See
http://conda.pydata.org/docs/custom-channels.html for more
information about channels. (default: conda-forge,r,bioconda,iuc).
information about channels. (default: bioconda,r,defaults,conda-forge,iuc).

auto_install
Set to True to instruct Galaxy to look for and install missing tool
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2 changes: 1 addition & 1 deletion lib/galaxy/tools/deps/resolvers/conda.py
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Expand Up @@ -31,7 +31,7 @@

DEFAULT_BASE_PATH_DIRECTORY = "_conda"
DEFAULT_CONDARC_OVERRIDE = "_condarc"
DEFAULT_ENSURE_CHANNELS = "conda-forge,r,bioconda,iuc"
DEFAULT_ENSURE_CHANNELS = "bioconda,r,defaults,conda-forge,iuc"

log = logging.getLogger(__name__)

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