Installing Bowtie 2

Procedure

Use PuTTY to log in to the server as the root user.
Use an SFTP tool to upload the installation packages of Bowtie 2, SIMDe, and sse2neon to the /path/to/BOWTIE2 directory.
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
```
Run the following command to copy the SIMDe files to Bowtie 2:
```
cp -a ../simde-0.7.0-rc-1/simde third_party/simde
```

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

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

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

Parent topic: Configuring the Compilation Environment