Installing Bowtie2

The Bowtie2 or Bowtie commands are required for TopHat data test in the PATH environment. Therefore, you need to install Bowtie2 first.

Use PuTTY to log in to the server as the root user.
Run the following command to switch to the Bowtie2 installation directory:
```
cd /path/to/BOWTIE2
```
Run the following command to decompress the Bowtie2 source code package:
```
unzip bowtie2-2.3.5.1-source.zip
```
Run the following command to switch to the directory generated after the package is decompressed:
```
cd bowtie2-2.3.5.1
```
Run the following command to decompress SIMDe:
```
unzip simde-master.zip
```
Run the following command to copy the SIMDe files to Bowtie2:
```
cp -a simde-master/simde bowtie2-2.3.5.1/third_party/simde/
```

Run the following commands to check whether the bowtie2-2.3.5.1/third_party/simde/simde/x86/sse2.h file exists:

cd /path/to/BOWTIE2/bowtie2-2.3.5.1/third_party/simde/simde/x86

-rw-r--r-- 1 root root 99060 Aug  5 04:12 sse2.h

Run the following command to switch to the bowtie2-2.3.5.1 directory:
```
cd /path/to/BOWTIE2/bowtie2-2.3.5.1
```
Run the following command to perform the compilation:
```
make NO_TBB=1 POPCNT_CAPABILITY=0 all
```
Run the following command to load environment variables:
```
export PATH=/path/to/BOWTIE2/bowtie2-2.3.5.1:$PATH
```

Parent topic: Configuring the Compilation Environment