How do I get POLYSOLVER?

We have recently created a Docker version of Polysolver which should be easy to use.Here are the instructions:

Setup and testing

1. Please see the attached pdf for how to set up Docker.  Once you are done, then do the following:

$ docker pull sachet/polysolver:v4

2. Download and unzip the attached test_docker folder. Let's say it exists in /home/developer. Then run the following commands:

$ docker run -d -P --name p1 -v /home/developer/test_docker:/home/test_docker sachet/polysolver:v4 bash /home/polysolver/scripts/shell_call_hla_type_test /home/polysolver/test/test.bam Unknown 1 hg19 STDFQ 0 /home/test_docker

You can actively monitor the files created in /home/developer/test_docker. In less than 5 minutes you should have a file called winners.hla.txt. The rest of the intermediate files should also have been cleaned.

3. Finally, to test if you had a successful run, do the following:

$ diff /home/developer/test_docker/orig.winners.hla.txt /home/developer/test_docker/winners.hla.txt

Notes:
1. Please make sure that you run the docker container with at least 4GB memory.
2. Please note that the shell_call_hla_type_test is for testing purposes only. When running (see below), use the shell_call_hla_type script.


Running

1. Please set the following variables on your machine:
(a). $DIR: directory on your local machine that has the exome BAM file. This is also the directory where all the intermediate files will be created by POLYSOLVER during running. The final output - called "winners.hla.txt" will be in this directory as well.
(b). $BAM: the name of your BAM file. Note: This is not the *path* to the file, just the name.
(c). $NAME: a name assigned to the container that is running the job. After the job has completed, i.e. after the winners.hla.txt file has been generated, please remove the container with the following command:
'docker rm $NAME'

2. Run the command:

'sudo docker run -d -P --name $NAME -v $DIR:/home/docker sachet/polysolver:v4 bash /home/polysolver/scripts/shell_call_hla_type /home/docker/$BAM Unknown 1 hg19 STDFQ 0 /home/docker'

3. After winners.hla.txt is generated:

'sudo docker rm $NAME'

Please write to sachet.shukla@gmail.com if you have any questions.