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Resolve conflicts in conda with priority to conda-forge #282

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Resolve conflicts in conda with priority to conda-forge #282

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2afad7a
Resolve conflicts in conda with priority to conda-forge
TomKellyGenetics Oct 2, 2020
d0c9c52
Update scripts/install_conda_env.sh
TomKellyGenetics Oct 7, 2020
740878d
Set python 3 version to 3.7
TomKellyGenetics Oct 27, 2020
658a076
Merge branch 'master' into patch-1
TomKellyGenetics Jun 12, 2021
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5 changes: 2 additions & 3 deletions scripts/install_conda_env.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,9 @@ echo "=== Checking conda version ==="
conda --version

echo "=== Installing pipeline's Conda environments ==="

if [[ "$1" == mamba ]]; then
conda install mamba -y -c conda-forge
mamba create -n ${CONDA_ENV_PY3} --file ${REQ_TXT_PY3} -y -c defaults -c r -c bioconda -c conda-forge
mamba create -n ${CONDA_ENV_PY3} --file ${REQ_TXT_PY3} -y -strict-channel-priority --override-channels -c default -c -r --c conda-forge -c bioconda
mamba create -n ${CONDA_ENV_PY2} --file ${REQ_TXT_PY2} -y -c defaults -c r -c bioconda -c conda-forge
else
echo
Expand All @@ -28,7 +27,7 @@ else
echo "If you get another conflict in the mamba installation step itself "
echo "Then you may need to clean-install miniconda3 and re-login."
echo
conda create -n ${CONDA_ENV_PY3} --file ${REQ_TXT_PY3} -y -c defaults -c r -c bioconda -c conda-forge
conda create -n ${CONDA_ENV_PY3} --file ${REQ_TXT_PY3} -y -strict-channel-priority --override-channels -c default -c -r --c conda-forge -c bioconda
conda create -n ${CONDA_ENV_PY2} --file ${REQ_TXT_PY2} -y -c defaults -c r -c bioconda -c conda-forge
fi

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4 changes: 3 additions & 1 deletion scripts/requirements.txt
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@@ -1,5 +1,7 @@
# for python3
# conda repos: defaults, r, bioconda, conda-forge
# conda repos: defaults, r, conda-forge, bioconda

python == 3.7.9

nomkl # using MKL can change MACS2 output randomly on different platforms

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