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Merged
jmchilton merged 1 commit into from
Sep 13, 2018
Merged

change the channel priority of conda (again) #867

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2 changes: 1 addition & 1 deletion docs/_writing_conda_init.rst
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Expand Up @@ -46,7 +46,7 @@
installing: requests-2.18.4-py36h4516966_1 ...
installing: conda-4.3.31-py36_0 ...
installation finished.
/Users/john/miniconda3/bin/conda install -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --channel r conda=4.3.33 conda-build=2.1.18
/Users/john/miniconda3/bin/conda install -y --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults conda=4.3.33 conda-build=2.1.18
Fetching package metadata ...................
Solving package specifications: .

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6 changes: 3 additions & 3 deletions docs/_writing_conda_search.rst
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Expand Up @@ -12,7 +12,7 @@ all the software and all the versions available matching that search term - incl
::

$ planemo conda_search seqt
/Users/john/miniconda3/bin/conda search --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults '*seqt*'
/Users/john/miniconda3/bin/conda search --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults '*seqt*'
Loading channels: done
# Name Version Build Channel
bioconductor-htseqtools 1.26.0 r3.4.1_0 bioconda
Expand All @@ -30,12 +30,12 @@ all the software and all the versions available matching that search term - incl
``conda search`` command but configured to use the same channels and other options as
Planemo and Galaxy. The following Conda command would also work to search::

$ $HOME/miniconda3/bin/conda -c iuc -c bioconda -c conda-forge '*seqt*'
$ $HOME/miniconda3/bin/conda -c iuc -c conda-forge -c bioconda '*seqt*'

For Conda versions 4.3.X or less, the search invocation would be something a bit
different::

$ $HOME/miniconda3/bin/conda -c iuc -c bioconda -c conda-forge seqt
$ $HOME/miniconda3/bin/conda -c iuc -c conda-forge -c bioconda seqt


Alternatively the Anaconda_ website can be used to search for packages. Typing ``seqtk``
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6 changes: 3 additions & 3 deletions docs/_writing_dependencies_containers.rst
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Expand Up @@ -152,16 +152,16 @@ demonstrating this - `bwa_and_samtools.xml
$ planemo project_init --template=conda_testing conda_testing
$ cd conda_testing/
$ planemo mull bwa_and_samtools.xml
/Users/john/.planemo/involucro -v=3 -f /Users/john/workspace/planemo/.venv/lib/python2.7/site-packages/galaxy_lib-17.9.0-py2.7.egg/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='iuc,bioconda,r,defaults,conda-forge' -set TEST='true' -set TARGETS='samtools=1.3.1,bwa=0.7.15' -set REPO='quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:03dc1d2818d9de56938078b8b78b82d967c1f820' -set BINDS='build/dist:/usr/local/' -set PREINSTALL='conda install --quiet --yes conda=4.3' build
/Users/john/.planemo/involucro -v=3 -f /Users/john/workspace/planemo/.venv/lib/python2.7/site-packages/galaxy_lib-17.9.0-py2.7.egg/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='iuc,bioconda,r,defaults,conda-forge' -set TEST='true' -set TARGETS='samtools=1.3.1,bwa=0.7.15' -set REPO='quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:03dc1d2818d9de56938078b8b78b82d967c1f820' -set BINDS='build/dist:/usr/local/' -set PREINSTALL='conda install --quiet --yes conda=4.3' build
/Users/john/.planemo/involucro -v=3 -f /Users/john/workspace/planemo/.venv/lib/python2.7/site-packages/galaxy_lib-17.9.0-py2.7.egg/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='iuc,conda-forge,bioconda,defaults' -set TEST='true' -set TARGETS='samtools=1.3.1,bwa=0.7.15' -set REPO='quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:03dc1d2818d9de56938078b8b78b82d967c1f820' -set BINDS='build/dist:/usr/local/' -set PREINSTALL='conda install --quiet --yes conda=4.3' build
/Users/john/.planemo/involucro -v=3 -f /Users/john/workspace/planemo/.venv/lib/python2.7/site-packages/galaxy_lib-17.9.0-py2.7.egg/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='iuc,conda-forge,bioconda,defaults' -set TEST='true' -set TARGETS='samtools=1.3.1,bwa=0.7.15' -set REPO='quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:03dc1d2818d9de56938078b8b78b82d967c1f820' -set BINDS='build/dist:/usr/local/' -set PREINSTALL='conda install --quiet --yes conda=4.3' build
[Jun 19 11:28:35] DEBU Run file [/Users/john/workspace/planemo/.venv/lib/python2.7/site-packages/galaxy_lib-17.9.0-py2.7.egg/galaxy/tools/deps/mulled/invfile.lua]
[Jun 19 11:28:35] STEP Run image [continuumio/miniconda:latest] with command [[rm -rf /data/dist]]
[Jun 19 11:28:35] DEBU Creating container [step-730a02d79e]
[Jun 19 11:28:35] DEBU Created container [5e4b5f83c455 step-730a02d79e], starting it
[Jun 19 11:28:35] DEBU Container [5e4b5f83c455 step-730a02d79e] started, waiting for completion
[Jun 19 11:28:36] DEBU Container [5e4b5f83c455 step-730a02d79e] completed with exit code [0] as expected
[Jun 19 11:28:36] DEBU Container [5e4b5f83c455 step-730a02d79e] removed
[Jun 19 11:28:36] STEP Run image [continuumio/miniconda:latest] with command [[/bin/sh -c conda install --quiet --yes conda=4.3 && conda install -c iuc -c bioconda -c r -c defaults -c conda-forge samtools=1.3.1 bwa=0.7.15 -p /usr/local --copy --yes --quiet]]
[Jun 19 11:28:36] STEP Run image [continuumio/miniconda:latest] with command [[/bin/sh -c conda install --quiet --yes conda=4.3 && conda install -c iuc -c conda-forge -c bioconda -c defaults samtools=1.3.1 bwa=0.7.15 -p /usr/local --copy --yes --quiet]]
[Jun 19 11:28:36] DEBU Creating container [step-e95bf001c8]
[Jun 19 11:28:36] DEBU Created container [72b9ca0e56f8 step-e95bf001c8], starting it
[Jun 19 11:28:37] DEBU Container [72b9ca0e56f8 step-e95bf001c8] started, waiting for completion
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2 changes: 1 addition & 1 deletion docs/installation.rst
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Expand Up @@ -47,8 +47,8 @@ Afterwards run the following commands.

::

$ conda config --add channels conda-forge
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ conda install planemo

Galaxy is known to have issues when running with a Conda Python so this approach
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2 changes: 1 addition & 1 deletion planemo/conda.py
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Expand Up @@ -19,7 +19,7 @@
MESSAGE_ERROR_CANNOT_INSTALL = "Cannot install Conda - perhaps due to a failed installation or permission problems."
MESSAGE_ERROR_NOT_INSTALLING = "Conda not configured - run ``planemo conda_init`` or pass ``--conda_auto_init`` to continue."

BEST_PRACTICE_CHANNELS = ["bioconda", "conda-forge", "defaults", "r"]
BEST_PRACTICE_CHANNELS = ["conda-forge", "bioconda", "defaults"]


def build_conda_context(ctx, **kwds):
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2 changes: 1 addition & 1 deletion planemo/options.py
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Expand Up @@ -531,7 +531,7 @@ def conda_ensure_channels_option():
use_env_var=True,
help=("Ensure conda is configured with specified comma separated "
"list of channels."),
default="iuc,bioconda,conda-forge,defaults",
default="iuc,conda-forge,bioconda,defaults",
)


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2 changes: 1 addition & 1 deletion scripts/update_bioconda.bash
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Expand Up @@ -51,7 +51,7 @@ sed -E -i "s/^ version: .*$/ version: \"$VERSION\"/" $METADATA
sed -E -i "s/^ url: .*$/ url: $URL/" $METADATA
sed -E -i "s/^ md5: .*$/ md5: $MD5SUM/" $METADATA

"$CONDA_EXEC" build "$RECIPE" --channel bioconda --channel conda-forge
"$CONDA_EXEC" build "$RECIPE" --channel conda-forge --channel bioconda
git add "$RECIPE/meta.yaml"
git add "$OLD_RECIPE"
git commit -m "Update $PACKAGE to version $VERSION"
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2 changes: 1 addition & 1 deletion tests/test_training.py
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Expand Up @@ -49,7 +49,7 @@
'conda_copy_dependencies': False,
'conda_debug': False,
'conda_dependency_resolution': False,
'conda_ensure_channels': 'iuc,bioconda,conda-forge,defaults',
'conda_ensure_channels': 'iuc,conda-forge,bioconda,defaults',
'conda_exec': None,
'conda_prefix': None,
'conda_use_local': False,
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