Compilation and Installation

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Decompress the KneadData installation package.

   cd /path/to/kneaddata
   unzip kneaddata-0.7.7-alpha.zip

3. Go to the directory generated after the decompression.

   cd kneaddata-0.7.7-alpha

4. Edit the setup.py file.
   1. Open the setup.py file.

      vi setup.py

   2. As shown in the following figure, add import shutil, which will be used when coping the Bowtie2 file.

      

   3. In the def download_unpack_zip module, add the following content:

      test1 = r'/path/to/Bowtie2/bowtie2-2.4.2-linux-aarch64.zip'
      shutil.copy(test1,download_file)

      

   4. Search for if not bowtie2_installed or replace_install.

      Comment out the two lines containing bowtie2-2.2.3-linux.x86_64.zip and add the following content:

      bowtie2_file="bowtie2-2.4.2-linux-aarch64.zip"
      bowtie2_url="http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.2/bowtie2-2.4.2-linux-aarch64.zip"

      Comment out bowtie2_folder="bowtie2-2.2.3" and add the following content:

      bowtie2_folder="bowtie2-2.4.2-linux-aarch64"

      

5. Start the installation.

   python setup.py install