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Update conda channel order to sync with Bioconda

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This commit is contained in:
Nicola Soranzo
2017-10-02 12:43:56 +01:00
parent cfabe37d69
commit 2eed478545
3 changed files with 8 additions and 5 deletions
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config/galaxy.ini.sample
+1 -2
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@@ -209,8 +209,7 @@ 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)
# the recommended channel order is the one from BioConda (https://github.com/bioconda/bioconda-recipes/blob/master/config.yml#L8)
#conda_ensure_channels = iuc,bioconda,r,defaults,conda-forge
#conda_ensure_channels = iuc,bioconda,conda-forge,defaults,r
# Set to True to instruct Galaxy to look for and install missing tool
# dependencies before each job runs.
#conda_auto_install = False
doc/source/admin/dependency_resolvers.rst
+2 -2
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@@ -220,8 +220,8 @@ debug
ensure_channels
conda channels to enable by default. See
http://conda.pydata.org/docs/custom-channels.html for more
information about channels. This defaults to ``iuc,bioconda,r,defaults,conda-forge``.
This order should be consistent with `Bioconda prescribed order <https://github.com/bioconda/bioconda-recipes/blob/master/config.yml#L8>`__
information about channels. This defaults to ``iuc,bioconda,conda-forge,defaults,r``.
This order should be consistent with the `Bioconda prescribed order <https://github.com/bioconda/bioconda-recipes/blob/master/config.yml>`__
if it includes ``bioconda``.
auto_install
lib/galaxy/tools/deps/resolvers/conda.py
+5 -1
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@@ -39,7 +39,11 @@ from ..resolvers import (
DEFAULT_BASE_PATH_DIRECTORY = "_conda"
DEFAULT_CONDARC_OVERRIDE = "_condarc"
DEFAULT_ENSURE_CHANNELS = "iuc,bioconda,r,defaults,conda-forge"
# Conda channel order from highest to lowest, following the one used in
# https://github.com/bioconda/bioconda-recipes/blob/master/config.yml , but
# adding `iuc` as first channel (for Galaxy-specific packages) and `r` as last
# (for old R packages)
DEFAULT_ENSURE_CHANNELS = "iuc,bioconda,conda-forge,defaults,r"
CONDA_SOURCE_CMD = """[ "$CONDA_DEFAULT_ENV" = "%s" ] ||
MAX_TRIES=3
COUNT=0