Installing Bowtie

Procedure

Use PuTTY to log in to the server as the root user.

Run the following command to install dependencies:

yum install zlib.aarch64 zlib-devel.aarch64 zlib-static.aarch64

Run the following command to decompress the installation package:
```
unzip bowtie-1.2.3.zip
```
Run the following command to switch to the directory that contains decompressed files:
```
cd /path/to/BOWTIE/bowtie-1.2.3
```
Run the following commands to modify the configuration file Makefile:
1. Open Makefile.
```
vi Makefile
```
2. Press i to enter the insert mode and modify the file as follows:
  To support AArch64, add the following information in bold to the end of about line 162:
```
BITS=32
ifeq (x86_64,$(shell uname -m))
BITS=64
endif
ifeq (aarch64,$(shell uname -m))
BITS=64
endif
```
  Modify the following content in about line 187:
```
DEBUG_FLAGS = -O0 -g3 
RELEASE_FLAGS = -O3 
NOASSERT_FLAGS = -DNDEBUG
FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
```
  Add the following content in bold after the commented lines to add the AArch64 branch:
```
M64_FLAGS := -m64
ifeq (aarch64,$(shell uname -m))
M64_FLAG :=
endif
```
3. Press Esc, type :wq!, and press Enter to save the file and exit.
Run the following commands to modify the alphabet.cpp file:
1. Open alphabet.cpp.
```
vi /path/to/BOWTIE/bowtie-1.2.3/alphabet.cpp
```
2. Press i to enter the insert mode and modify line 276 of the file.
  Before the modification:
```
char mask2iupac[16] = {...}
```
  After the modification:
```
signed char mask2iupac[16] = {...}
```
3. Press Esc, type :wq!, and press Enter to save the file and exit.
Run the following command to create a folder:
```
mkdir -p ./third_party/simde/simde/x86
```
Run the following command to perform the configuration:
```
export NO_TBB=1
export POPCNT_CAPABILITY=0
```
Run the following command to decompress the SIMDE installation package:
```
unzip simde-master.zip
```
Run the following command to copy the simde directory in simde-master to bowtie-1.2.3/third_party/simde/:
```
cp -a  simde-master/simde  /path/to/BOWTIE/bowtie-1.2.3/third_party/simde/
```
Run the following command to decompress the sse2neno installation package:
```
unzip sse2neon-master.zip
```
Run the following command to copy the SSE2NEON.h file to bowtie-1.2.3/third_party/simde/simde/x86/:
```
cp -a sse2neon-master/SSE2NEON.h  /path/to/BOWTIE/bowtie-1.2.3/third_party/simde/simde/x86/
```
Run the following command to perform the compilation:
```
cd /path/to/BOWTIE/bowtie-1.2.3
make
```
Run the following command to perform the installation:
```
make install
```
Run the following command to set environment variables:
export PATH=/path/to/BOWTIE/bowtie-1.2.3:$PATH

Parent topic: Compiling and Installing Bowtie