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 set the following variables on your machine: 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.
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