MetaHipMer2：从头组装宏基因组

Terabase-scale metagenome coassembly with MetaHipMer | Scientific Reports

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf369/8126258

安装

配置环境

berkeleylab / upcxx / wiki / INSTALL — Bitbucket

mamba create -n mhm2_env -c conda-forge \
  cmake \
  gxx_linux-64 \
  upcxx \
  make \
  git \
  cuda-toolkit=11.7  # 如果你需要 GPU 支持

wget -c https://bitbucket.org/berkeleylab/upcxx/downloads/upcxx-2023.9.0.tar.gz
tar -xvzf upcxx-2023.9.0.tar.gz
conda activate mhm2_env
cd upcxx-2023.9.0/
mkdir install
./configure --prefix=path/upcxx-2023.9.0/install/ --with-cxx=mpic++ --enable-smp
gmake all
# gmake check #optional
make install NETWORK=smp

vim ~/.bashrc
#写入
export PATH=/home/zhongpei/hard_disk_sda2/zhongpei/Software/MetaHipMer2/upcxx-2023.9.0/install/bin:$PATH
#保存退出
source ~/.bashrc
which upcxx
git submodule init
git submodule update

cd ~/Software/MetaHipMer2
# 网络不好
# git clone --recurse-submodules https://bitbucket.org/berkeleylab/mhm2.git
wget -c https://bitbucket.org/berkeleylab/mhm2/downloads/mhm2-v2.2.1.0.tar.gz
tar -xzvf mhm2-v2.2.1.0.tar.gz
cd mhm2-v2.2.1.0
chmod 755 ./build.sh
# 修改./build.sh
# 将 cmake $rootdir -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCMAKE_BUILD_TYPE=$1 -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH \
      -DMHM2_ENABLE_TESTING=$testing -DCMAKE_CXX_FLAGS="-Wno-deprecated-declarations" $MHM2_CMAKE_EXTRAS $ADDITIONAL_PARMS
# 修改为 cmake $rootdir -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCMAKE_BUILD_TYPE=$1 -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH \
      -DMHM2_ENABLE_TESTING=$testing -DCMAKE_CXX_COMPILER=/usr/bin/mpic++ \
      -DCMAKE_CXX_FLAGS="-Wno-deprecated-declarations" $MHM2_CMAKE_EXTRAS $ADDITIONAL_PARMS

# ./build.sh cleanall #如果报错可以试试这个
./build.sh Release

mhm2-v2.2.1.0/install/bin/mhm2.py -h
# 可以了！