From 2afad7a122850c31a1308704b04c8c8ffd7a2a8c Mon Sep 17 00:00:00 2001 From: Tom Kelly Date: Fri, 2 Oct 2020 23:18:12 +0900 Subject: [PATCH 1/3] Resolve conflicts in conda with priority to conda-forge See issue here: https://github.com/bioconda/bioconda-recipes/issues/17186 --- scripts/install_conda_env.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/install_conda_env.sh b/scripts/install_conda_env.sh index f1026854..e90ec948 100755 --- a/scripts/install_conda_env.sh +++ b/scripts/install_conda_env.sh @@ -12,7 +12,7 @@ SRC_DIR=${SH_SCRIPT_DIR}/../src conda --version # check if conda exists echo "=== Installing pipeline's Conda environments ===" -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 --channel conda-forge --channel bioconda -c r -c defaults conda create -n ${CONDA_ENV_PY2} --file ${REQ_TXT_PY2} -y -c defaults -c r -c bioconda -c conda-forge echo "=== Configuring for pipeline's Conda environments ===" From d0c9c52bbebf197c25edd2152a5ccdbae09427c6 Mon Sep 17 00:00:00 2001 From: Tom Kelly Date: Wed, 7 Oct 2020 10:58:03 +0900 Subject: [PATCH 2/3] Update scripts/install_conda_env.sh --- scripts/install_conda_env.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/install_conda_env.sh b/scripts/install_conda_env.sh index e90ec948..187c3711 100755 --- a/scripts/install_conda_env.sh +++ b/scripts/install_conda_env.sh @@ -12,7 +12,7 @@ SRC_DIR=${SH_SCRIPT_DIR}/../src conda --version # check if conda exists echo "=== Installing pipeline's Conda environments ===" -conda create -n ${CONDA_ENV_PY3} --file ${REQ_TXT_PY3} -y -strict-channel-priority --override-channels --channel conda-forge --channel bioconda -c r -c defaults +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 echo "=== Configuring for pipeline's Conda environments ===" From 740878d696a8c0be422cf0e021a34af45e195448 Mon Sep 17 00:00:00 2001 From: Tom Kelly Date: Tue, 27 Oct 2020 11:02:41 +0900 Subject: [PATCH 3/3] Set python 3 version to 3.7 --- scripts/requirements.txt | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/scripts/requirements.txt b/scripts/requirements.txt index 4fea42de..43faae41 100644 --- a/scripts/requirements.txt +++ b/scripts/requirements.txt @@ -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