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reverse conda env handling (fix for #114) #122

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Merged
ewels merged 3 commits into from
Aug 10, 2018
Merged

reverse conda env handling (fix for #114) #122

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ecb93b6
reverse conda env handling (fix for #114)
HadrienG Aug 9, 2018
6936fb3
update test files
HadrienG Aug 10, 2018
9b43297
more tests are expected to fail (due to ENV line)
HadrienG Aug 10, 2018
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7 changes: 5 additions & 2 deletions nf_core/lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -557,7 +557,8 @@ def check_conda_dockerfile(self):
expected_strings = [
'FROM nfcore/base',
'COPY environment.yml /',
'RUN conda env update -n root -f /environment.yml && conda clean -a'
'RUN conda env create -f /environment.yml && conda clean -a',
'ENV PATH /opt/conda/envs/{}/bin:$PATH'.format(self.conda_config['name'])
]

difference = set(expected_strings) - set(self.dockerfile)
Expand All @@ -581,8 +582,10 @@ def check_conda_singularityfile(self):
'From:nfcore/base',
'Bootstrap:docker',
'VERSION {}'.format(self.config['params.version'].strip(' \'"')),
'PATH=/opt/conda/envs/{}/bin:$PATH'.format(self.conda_config['name']),
'export PATH',
'environment.yml /',
'/opt/conda/bin/conda env update -n root -f /environment.yml',
'/opt/conda/bin/conda env create -f /environment.yml',
'/opt/conda/bin/conda clean -a',
]

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3 changes: 2 additions & 1 deletion tests/lint_examples/minimal_working_example/Dockerfile
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Expand Up @@ -4,4 +4,5 @@ LABEL authors="[email protected]" \
description="Docker image containing all requirements for the nf-core tools pipeline"

COPY environment.yml /
RUN conda env update -n root -f /environment.yml && conda clean -a
RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/nfcore-tools-0.4/bin:$PATH
6 changes: 5 additions & 1 deletion tests/lint_examples/minimal_working_example/Singularity
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Expand Up @@ -6,9 +6,13 @@ Bootstrap:docker
DESCRIPTION Container image containing all requirements for the nf-core/tools pipeline
VERSION 0.4

%environment
PATH=/opt/conda/envs/nfcore-tools-0.4/bin:$PATH
export PATH

%files
environment.yml /

%post
/opt/conda/bin/conda env update -n root -f /environment.yml
/opt/conda/bin/conda env create -f /environment.yml
/opt/conda/bin/conda clean -a
2 changes: 1 addition & 1 deletion tests/test_lint.py
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Expand Up @@ -321,7 +321,7 @@ def test_conda_dockerfile_fail(self):
lint_obj.conda_config['name'] = 'nfcore-tools-0.4'
lint_obj.dockerfile = ['fubar']
lint_obj.check_conda_dockerfile()
expectations = {"failed": 3, "warned": 0, "passed": 0}
expectations = {"failed": 4, "warned": 0, "passed": 0}
self.assess_lint_status(lint_obj, **expectations)

def test_conda_dockerfile_skip(self):
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