Compilation and Installation

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Create and enable the conda environment for kb_python.

   conda activate base
   conda create -n kb
   conda activate kb
   conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
   conda config --add channels conda-forge
   conda config --set show_channel_urls yes
   conda update -n base -c defaults conda

   

   conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/ is optional. If the network speed is slow when conda is used to install the software, you can run this command to add a conda source from China.

3. Install the Python environment.

   conda install python=3.8
   pip install Cython --trusted-host mirrors.tools.huawei.com -i http://mirrors.tools.huawei.com/pypi/simple

4. Install PYSAM.

   cd /home
   git clone https://github.com/pysam-developers/pysam.git
   cd pysam
   yum install zlib-devel
   yum install bzip2-devel
   python setup.py install

5. Install tables.

   conda install h5py python-blosc
   pip install tables

6. Install kb-python.

   cd /home/kb_python
   pip install -r requirements.txt
   pip install -r dev-requirements.txt
   python setup.py install

7. Verify kb-python.

   kb info

   If the following information is displayed, kb-python is successfully installed.

   

   • For error message "OSError: [Errno 8] Exec format error: '/root/anaconda3/envs/kb/lib/python3.8/site-packages/kb_python-0.26.4 -py3.8.egg/kb_python/bins/linux/kallisto/kallisto'", run the following command:

     ln -sf /usr/local/bin/bustools /root/anaconda3/envs/kb/lib/python3.8/site-packages/kb_python-0.26.4-py3.8.egg/kb_python/bins/linux/bustools/bustools

   • For error message "OSError: [Errno 8] Exec format error: '/root/anaconda3/envs/kb/lib/python3.8/site-packages/kb_python-0.26.4-py3.8.egg/kb_python/bins/linux/bustools/bustools'", run the following command:

     ln -sf /usr/local/bin/kallisto /root/anaconda3/envs/kb/lib/python3.8/site-packages/kb_python-0.26.4-py3.8.egg/kb_python/bins/linux/kallisto/kallsto