From 1764fd1732da65786ddbcf9468c3a82fc8b08f0e Mon Sep 17 00:00:00 2001 From: Marcel Bargull Date: Sun, 5 May 2024 12:38:31 +0200 Subject: [PATCH 1/2] update to bioconda-utils v2.15.0 Signed-off-by: Marcel Bargull --- common.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/common.sh b/common.sh index 1bc6c85..6748f37 100644 --- a/common.sh +++ b/common.sh @@ -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" From a69b0a4c75d0a98fb4d8ffa4cd7d5754ff053579 Mon Sep 17 00:00:00 2001 From: Marcel Bargull Date: Sun, 5 May 2024 16:55:39 +0200 Subject: [PATCH 2/2] Fix conda index call; replace mamba with conda Signed-off-by: Marcel Bargull --- install-and-set-up-conda.sh | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/install-and-set-up-conda.sh b/install-and-set-up-conda.sh index 3defe66..8e29135 100644 --- a/install-and-set-up-conda.sh +++ b/install-and-set-up-conda.sh @@ -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) @@ -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 $MAMBAFORGE_INSTALLATION_DIR) @@ -67,8 +64,6 @@ export PATH="${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. @@ -78,9 +73,9 @@ 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 @@ -88,7 +83,9 @@ if [ ${BIOCONDA_DISABLE_BUILD_PREP:=0} == 0 ]; then # Set local channel as highest priority (requires conda-build, which is # installed as a dependency of bioconda-utils) mkdir -p "${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