Installing Samtools

Procedure

Use PuTTY to log in to the server as the root user.
Run the following command to go to the SAMtools installation directory:
```
cd /path/to/SAMTOOL
```
Run the following command to decompress the SAMtools installation package:
Install SAMtools and HTSlib separately. Do not use SAMtools that contains HTSlib. Otherwise, errors may occur during compilation.
```
tar -xvf samtools-0.1.19.tar.gz
```
Run the following command to switch to the directory generated after the package is decompressed:
```
cd samtools-0.1.19
```
Run the following command to obtain the GNU absolute directory:
```
which gcc
```
Modify the Makefile file.
1. Open Makefile.
```
vi Makefile
```
2. Press i to enter the insert mode and modify the file as follows:
  Before the modification:
```
CC     = gcc 
```
  After the modification:
```
CC     = /path/to/GNU/bin/gcc 
```
3. Press Esc, type :wq!, and press Enter to save the file and exit.
Run the following commands to perform compilation and installation:
```
make
```

Run the following commands to copy the generated binary files to the default path of the root directory so that Cufflinks can directly identify the SAMtools and HTSlib files:

mkdir /usr/local/include/bam
cp /path/to/SAMTOOL/samtools-0.1.19/libbam.a /usr/local/lib
cp /path/to/SAMTOOL/samtools-0.1.19/*.h /usr/local/include/bam/
cp /path/to/SAMTOOL/samtools-0.1.19/samtools /usr/bin/

Parent topic: Configuring the Compilation Environment