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update to bioconda-utils v2.15.0 #52

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May 5, 2024
Merged

update to bioconda-utils v2.15.0 #52

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1764fd1
update to bioconda-utils v2.15.0
mbargull May 5, 2024
a69b0a4
Fix conda index call; replace mamba with conda
mbargull May 5, 2024
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4 changes: 2 additions & 2 deletions common.sh
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
BIOCONDA_UTILS_TAG=v2.14.0
MAMBAFORGE_VER=23.1.0-1
BIOCONDA_UTILS_TAG=v2.15.0
MAMBAFORGE_VER=24.3.0-0
MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge"
13 changes: 5 additions & 8 deletions install-and-set-up-conda.sh
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Expand Up @@ -5,7 +5,6 @@ set -e
# - Installs mambaforge to ${HOME}/mambaforge. Version is determined by common.sh,
# which is downloaded at runtime.
# - Sets channel order and sets strict channel priority
# - Installs mamba into the base env
# - Installs bioconda-utils into a "bioconda" env (unless
# $BIOCONDA_DISABLE_BUILD_PREP=1). Version is determined by common.sh.
# - Sets up local channel to have highest priority (unless $BIOCONDA_DISABLE_BUILD_PREP=1)
Expand Down Expand Up @@ -44,8 +43,6 @@ if [[ $(uname) == "Darwin" ]]; then
sudo chown -R $USER $(dirname $MAMBAFORGE_INSTALLATION_DIR)

# conda-forge-ci-setup does some additional setup for Mac.
# Installing bioconda-utils and conda-forge-ci-setup with conda causes dependency conflicts.
# Installing bioconda-utils and conda-forge-ci-setup with mamba works fine.
BIOCONDA_ADDITIONAL_INSTALL_PKGS="conda-forge-ci-setup"
else
mkdir -p $(dirname $MAMBAFORGE_INSTALLATION_DIR)
Expand All @@ -67,8 +64,6 @@ export PATH="${MAMBAFORGE_INSTALLATION_DIR}/bin:${PATH}"
# disable build preparation here because we don't yet have the local channel from conda-build
BIOCONDA_DISABLE_BUILD_PREP=1 bash configure-conda.sh

mamba install mamba -y

# By default, for building packages, we install bioconda-utils. However when
# testing bioconda-utils itself, we don't want to install a release, in
# which case set BIOCONDA_DISABLE_BUILD_PREP to a non-zero value.
Expand All @@ -78,17 +73,19 @@ if [ ${BIOCONDA_DISABLE_BUILD_PREP:=0} == 0 ]; then
source ${MAMBAFORGE_INSTALLATION_DIR}/etc/profile.d/mamba.sh

# set up env with all dependencies
mamba create -n bioconda -y --file https://raw.githubusercontent.com/bioconda/bioconda-utils/$BIOCONDA_UTILS_TAG/bioconda_utils/bioconda_utils-requirements.txt $BIOCONDA_ADDITIONAL_INSTALL_PKGS
conda create -n bioconda -y --file https://raw.githubusercontent.com/bioconda/bioconda-utils/$BIOCONDA_UTILS_TAG/bioconda_utils/bioconda_utils-requirements.txt $BIOCONDA_ADDITIONAL_INSTALL_PKGS

mamba activate bioconda
conda activate bioconda

# install bioconda-utils itself via pip (this way we don't always have to wait for the conda package to be built before being able to fix things here)
pip install git+https://github.com/bioconda/bioconda-utils.git@$BIOCONDA_UTILS_TAG

# Set local channel as highest priority (requires conda-build, which is
# installed as a dependency of bioconda-utils)
mkdir -p "${MAMBAFORGE_INSTALLATION_DIR}/conda-bld/{noarch,linux-64,osx-64,linux-aarch64,osx-arm64}"
conda index "${MAMBAFORGE_INSTALLATION_DIR}/conda-bld"
# The base installation does not include conda-index, so use "command conda" to run bioconda
# env's "conda index".
command conda index "${MAMBAFORGE_INSTALLATION_DIR}/conda-bld"
conda config --add channels "file://${MAMBAFORGE_INSTALLATION_DIR}/conda-bld"
fi

Expand Down
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