Installing Bowtie 2

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Use an SFTP tool to upload the installation packages of Bowtie 2, SIMDe, and sse2neon to the /path/to/BOWTIE2 directory.
3. Run the following commands to decompress the installation package and go to the directory generated after the decompression:

   cd /path/to/BOWTIE2
   unzip bowtie2-2.3.5.1-source.zip
   tar -zxf v0.7.0-rc-1.tar.gz
   unzip master.zip
   cd bowtie2-2.3.5.1

4. Run the following command to copy the SIMDe files to Bowtie 2:

   cp -a ../simde-0.7.0-rc-1/simde third_party/simde

5. Run the following command to copy the sse2neon.h file to Bowtie 2:

   cp -a ../sse2neon-master/SSE2NEON.h third_party/simde/simde/x86/

6. Run the following command to perform the compilation:

   CC=`which gcc` CXX=`which g++` CXXFLAGS='-O3 -march=armv8.2-a -mtune=tsv110' CFLAGS='-O3 -march=armv8.2-a -mtune=tsv110' make NO_TBB=1 POPCNT_CAPABILITY=0 all