From 2eed478545857ab2c3b4c958bc3e2c360656af42 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Thu, 10 Aug 2017 16:04:26 +0100 Subject: [PATCH] Update conda channel order to sync with Bioconda --- config/galaxy.ini.sample | 3 +-- doc/source/admin/dependency_resolvers.rst | 4 ++-- lib/galaxy/tools/deps/resolvers/conda.py | 6 +++++- 3 files changed, 8 insertions(+), 5 deletions(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 5720c826698d..3c0ea4283e11 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -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 diff --git a/doc/source/admin/dependency_resolvers.rst b/doc/source/admin/dependency_resolvers.rst index 0d6930d1ef79..12e93a773573 100644 --- a/doc/source/admin/dependency_resolvers.rst +++ b/doc/source/admin/dependency_resolvers.rst @@ -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 `__ + information about channels. This defaults to ``iuc,bioconda,conda-forge,defaults,r``. + This order should be consistent with the `Bioconda prescribed order `__ if it includes ``bioconda``. auto_install diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py index 908fb1cef083..caa8dd5bbb09 100644 --- a/lib/galaxy/tools/deps/resolvers/conda.py +++ b/lib/galaxy/tools/deps/resolvers/conda.py @@ -39,7 +39,11 @@ 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