Running and Installing Picard

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Install dependencies.

   yum install ncurses-devel.aarch64 bzip2-devel.aarch64 xz-devel.aarch64 java-1.8.0-openjdk-devel.aarch64 -y

3. Go to the Samtools directory.

   cd /path/to/SAMTOOLS

4. Decompress the Samtools package.

   tar -xvf samtools-0.1.9.tar.gz

5. Go to the directory generated after decompression.

   cd samtools-0.1.9

6. Obtain the absolute path of GNU.

   which gcc

7. 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.
8. Perform the compilation and installation.

   make

9. Add the Samtools environment variable.

   export PATH=/path/to/SAMTOOLS/samtools-0.1.9:$PATH

10. Go to the Picard directory.

    cd /path/to/PICARD

11. Test the Picard environment.

    java -jar picard.jar

    If the following information is displayed, the environment is normal.