tanyaphung/run_hla_polysolver

run_hla_polysolver

In this repo, I'm describing how to get the tool HLA polysolver (https://software.broadinstitute.org/cancer/cga/polysolver) to work. I spent a few hours figuring out how to get all the dependencies to run the software within a conda environment. I also found a couple of bugs in the codes (from the version that I downloaded) so I hope this step by step guide will help others as well.

Step 1: Download POLYSOLVER

• After creating an account, navigate to https://software.broadinstitute.org/cancer/cga/polysolver_download. Scroll down to the end of the page, you will see an option to download the software. Since I will be running this on a cluster, I right-clicked to copy the link address.

• Then, from your terminal, do:

wget https://software.broadinstitute.org/cancer/cga/sites/default/files/data/tools/polysolver/polysolver_v1.0.tar.gz
tar -xzvf polysolver_v1.0.tar.gz

• Now there should be a directory called polysolver. Change into that directory:

cd polysolver/

Step 2: Install the dependencies

• I use conda environment for this. I used miniconda. For instructions on how to install miniconda, see https://conda.io/en/master/miniconda.html

• We will create a conda environment called polysolver and install the necessay dependencies.

conda create --name polysolver
conda install -c anaconda perl 
conda install -c bioconda samtools=1.9 novoalign=3.06.05 perl-array-utils=0.5 perl-parallel-forkmanager=2.02 perl-list-moreutils=0.428 perl-bioperl
conda install -c cyclus java-jdk

• Activate the conda environment:

conda activate polysolver

• Download picard

wget https://github.com/broadinstitute/picard/releases/download/1.120/picard-tools-1.120.zip
unzip picard-tools-1.120.zip

Step 3: Edit the config file

• The default config.sh file (can be found in scripts/) use setenv but this commmand is for (t)csh. I am using bash so I have changed the config file to use export instead.
• The default config.sh file asks to give the directory to GATK. It actually looks for picard so you should give the path to the picard file that you downloaded in step 2.
• The config file I use can be found in this repo.

Step 4: Edit some other paths

• Type this into the terminal:

sed -i "s|/usr/bin/perl|$(which perl)|" scripts/*

• Without this, an error called undefined symbol: Perl_xs_handshake will be invoked.

Step 5: Edit the script shell_first_allele_calculations

• With the version of polysolver that I downloaded, there is a bug in the script shell_first_allele_calculations.

  • In the line SAMTOOLS sort -n $outDir/temp.$i.bam $outDir/nv.complete.chr6region.R0k6.csorted.REF_$i, the output symbol > is missing and the output file should be .bam.
  • To fix this, do:

  vim scripts/shell_first_allele_calculations
  $SAMTOOLS sort -n $outDir/temp.$i.bam >  $outDir/nv.complete.chr6region.R0k6.csorted.REF_$i.bam
  

  • If you don't do this, an error will be invoked, such as saying that the file nv.complete.chr6region.R0k6.csorted.REF_hla_c_18_06 does not exist

Step 6: Run

source scripts/config.sh
PERL5LIB=/home/tphung3/softwares/miniconda3/envs/polysolver/lib/site_perl/5.26.2/ scripts/shell_call_hla_type test/test.bam Unknown 1 hg19 STDFQ 0 out