Implementation and Use of Docker

In order to run the GPSRdocker, follow the below mentioned steps.

1. Install the docker into your system and create account at docker hub.

2. Make sure the docker is running before installing GPSR_2.0.

3. Once your docker is running fine, pull the docker image “gpsraghava” using the command "docker pull raghavagps/gpsrdocker"

4. Now enter into the docker image by running the command "docker run -i -t raghavagps/gpsraghava"

5. Once you are into the container, you will see there are minimum required libraries are provided which are required for running the standalone software. You can see this by running the command "ls"

6. Go the folder “gpsr” using the command "cd gpsr/".

7. In the folder gpsr, we have the Perl script “” along with the “list” file. This perl script is the main script which user needs to run. Run the code, using command /usr/bin/perl

8. As shown in Figure 4, system will ask to quit the system by typing “q” or to continue by pressing any key .

9. To download the required software, press any key other than ‘q’. This will show you the name of the software. Enter the serial number mentioned before the software to download it.

10. Once the user press the enter button, required software and other packages needed, will be downloaded automatically and will get installed into their respective directories. Go to that software folder.

11. Once you enter into the software folder, you will see a perl script by the name of the software.

12. If user don't know how to run the code, he/she can just simply run the command "/usr/bin/perl" .

13. Once user has the input file in FASTA format, by providing the full path of the input file.

14. Once the code is finished, it will generate the output file containing prediction result.

15. Once the user finishes the job, they can save the result by saving the current docker image into new image.

16. If in future, user wants to check the result, he/she can just open this image by command "docker run -i -t premier_result" .

Click here to download GPSRdocker manual


About Raghava

Professor Gajendra P.S. Raghava, Indraprasta Institute of Information Technology, New Delhi is a strong supporter of open source software and open access, all resources developed at his group are free for scientific use.