From b23abfc3db51bf7eca5feea4dd2ec110a74489ea Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Fri, 1 Sep 2023 15:25:25 -0700 Subject: [PATCH] Update README.md (#471) * Update README.md We've noticed locally some issues can come up if conda-forge isn't part of the channel list Just adding it in the conda install command in case * CI Fixes --- README.md | 4 ++-- azure-pipelines.yml | 34 ++++++++++++++++++++++++++-------- 2 files changed, 28 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index af3dc9bd..b2fe7f6c 100644 --- a/README.md +++ b/README.md @@ -54,13 +54,13 @@ Installation If you have the [Conda](https://docs.conda.io/en/latest/) package manager (Linux, MacOS) installed, run: - conda install -c bioconda abyss + conda install -c bioconda -c conda-forge abyss Or you can install ABySS in a dedicated environment: conda create -n abyss-env conda activate abyss-env - conda install -c bioconda abyss + conda install -c bioconda -c conda-forge abyss ## Install ABySS using Homebrew diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 07e76802..1da7708d 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -4,8 +4,8 @@ jobs: vmImage: macOS-11 steps: - script: | + rm -f /usr/local/bin/2to3-3.11 # brew is having issues with installing Python rm -f /usr/local/bin/2to3 # brew is having issues with installing Python - brew update brew install automake boost openmpi google-sparsehash make pandoc ghc gcc@12 displayName: Install common - script: | @@ -64,7 +64,7 @@ jobs: - script: | source activate abyss_CI conda install --yes -c conda-forge mamba python=3.9 - mamba install --yes -c conda-forge -c bioconda compilers make boost-cpp sparsehash openmpi automake perl btllib pandoc + mamba install --yes -c conda-forge -c bioconda clangxx_osx-64 make boost-cpp sparsehash openmpi automake perl btllib pandoc displayName: Install dependencies - script: | source activate abyss_CI @@ -73,7 +73,7 @@ jobs: export DISTCHECK_CONFIGURE_FLAGS="CC=clang CXX=clang++" ./autogen.sh ./configure - make -j12 distcheck + make -j12 distcheck AM_CXXFLAGS=-Wno-error=unused-but-set-variable displayName: Compiling ABySS - job: @@ -88,15 +88,24 @@ jobs: - script: | source activate abyss_CI conda install --yes -c conda-forge mamba python=3.9 - mamba install --yes -c conda-forge -c bioconda compilers=1.5.2 make boost-cpp sparsehash openmpi automake perl btllib pandoc + mamba install --yes -c conda-forge -c bioconda compilers=1.5.2 make boost-cpp sparsehash openmpi automake perl pandoc displayName: Install dependencies - script: | source activate abyss_CI + wget https://github.com/bcgsc/btllib/releases/download/v1.6.2/btllib-1.6.2.tar.gz + tar xzf btllib-1.6.2.tar.gz + cd btllib-1.6.2 export CC=clang export CXX=clang++ - export DISTCHECK_CONFIGURE_FLAGS="CC=clang CXX=clang++" + ./compile + displayName: Install btllib + - script: | + source activate abyss_CI + export CC=clang + export CXX=clang++ + export DISTCHECK_CONFIGURE_FLAGS="CC=clang CXX=clang++ --with-btllib=/Users/runner/work/1/s/btllib-1.6.2/install" ./autogen.sh - ./configure + ./configure --with-btllib=/Users/runner/work/1/s/btllib-1.6.2/install make -j12 distcheck displayName: Compiling ABySS @@ -116,11 +125,20 @@ jobs: displayName: Install dependencies - script: | source activate abyss_CI + wget https://github.com/bcgsc/btllib/releases/download/v1.6.2/btllib-1.6.2.tar.gz + tar xzf btllib-1.6.2.tar.gz + cd btllib-1.6.2 export CC=clang export CXX=clang++ - export DISTCHECK_CONFIGURE_FLAGS="CC=clang CXX=clang++" + ./compile + displayName: Install btllib + - script: | + source activate abyss_CI + export CC=clang + export CXX=clang++ + export DISTCHECK_CONFIGURE_FLAGS="CC=clang CXX=clang++ --with-btllib=/Users/runner/work/1/s/btllib-1.6.2/install" ./autogen.sh - ./configure + ./configure --with-btllib=/Users/runner/work/1/s/btllib-1.6.2/install make -j12 distcheck displayName: Compiling ABySS with clang 13