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Singularity image of Polysolver

First of all, install Singularity.

Building/getting the Singularity image of Polysolver

To build the Singularity image of Polysolver, run:

sudo singularity build polysolver-singularity_v4.sif Singularity.v4

To pull the Singularity image of Polysolver from Singularity Hub, run:

singularity pull shub://IARCbioinfo/polysolver-singularity:v4

The Singularity.v4 file instructs Singularity to build an image of Polysolver version 4 coming from the Docker Hub repository of its author.

It also instructs Singularity to perform some changes on the image in order to make the HLA typing functionality of Polysolver working.

To do so, the Polysolver script shell_call_hla_type located (in the image) at /home/polysolver/scripts/ needs a couple of modifications, as described below for information (these modifications are done by the Singularity.v4 file during the build).

The Singularity.v4 file

First of all, creates (in the image) a directory where users can bind-mount (see the -B option of singularity exec) their data, and also output their results (see the outDir argument of shell_call_hla_type):

mkdir /data

The script shell_call_hla_type is a bash script, so the shebang should point to bash, not to sh:

sed -i 's.#!/bin/sh.#!/bin/bash.g' /home/polysolver/scripts/shell_call_hla_type

In the image, the temporary directory should be /tmp:

sed -i 's.TMP_DIR=\$outDir.TMP_DIR=/tmp.g' /home/polysolver/scripts/shell_call_hla_type
sed -i 's.TMP_DIR=/home/polysolver.TMP_DIR=/tmp.g' /home/polysolver/scripts/shell_call_hla_type

The variable SAMTOOLS_DIR is not defined and is actually /home/polysolver/binaries:

sed -i 's.\$SAMTOOLS_DIR./home/polysolver/binaries.g' /home/polysolver/scripts/shell_call_hla_type

In hg38, the chromosome 6 is named chr6, not 6:

sed -i 's.6:29941260-29945884.chr6:29941260-29945884.g' /home/polysolver/scripts/shell_call_hla_type
sed -i 's.6:31353872-31357187.chr6:31353872-31357187.g' /home/polysolver/scripts/shell_call_hla_type
sed -i 's.6:31268749-31272105.chr6:31268749-31272105.g' /home/polysolver/scripts/shell_call_hla_type

Running the HLA typing functionality of Polysolver

Once the Singularity image polysolver-singularity_v4.sif built using the Singularity.v4 file as described above (or pulled from Singularity Hub), one can execute the shell_call_hla_type script as follows:

singularity exec -C \
-B /path/to/your/data/folder:/data \
-B /path/to/your/temporary/folder:/tmp \
polysolver-singularity_v4.sif /home/polysolver/scripts/shell_call_hla_type \
/data/yourBamFile.bam race includeFreq build format insertCalc /data

The -C option of singularity exec can prevent (if any) unwanted interferences between your system and the one within the image by running in an "isolated" mode.

The -B option of singularity exec mounts a folder of your system somewhere into the image, making its content available for the image.

In the above example, yourBamFile.bam is in the /path/to/your/data/folder/ directory of your system, and is mounted at /data in the image.

Consequently, in the image (and therefore for Polysolver), yourBamFile.bam is in the /data/ folder.

The same applies for the temporary directory: the image polysolver-singularity_v4.sif will use a folder of your system (/path/to/your/temporary/folder/ in the above example) as temporary directory.

For the remaining arguments passed to shell_call_hla_type, see below or run it without arguments:

Usage: /home/polysolver/scripts/shell_call_hla_type bam race includeFreq build format insertCalc outDir
    -bam: path to the BAM file to be used for HLA typing
    -race: ethnicity of the individual (Caucasian, Black, Asian or Unknown)
    -includeFreq: flag indicating whether population-level allele frequencies should be used as priors (0 or 1)
    -build: reference genome used in the BAM file (hg18, hg19 or hg38)
    -format: fastq format (STDFQ, ILMFQ, ILM1.8 or SLXFQ; see Novoalign documentation)
    -insertCalc: flag indicating whether empirical insert size distribution should be used in the model (0 or 1)
    -outDir: output directory

Other Polysolver modules

WARNING: only the HLA typing functionality of Polysolver was tested. The two other modules might work using something like:

POLYSOLVER-based mutation detection

singularity exec -C \
-B /path/to/your/data/directory_with_bams_and_winners_hla_file:/data \
-B /path/to/your/temporary/folder:/tmp \
polysolver-singularity_v4.sif /home/polysolver/scripts/shell_call_hla_mutations_from_type \
/data/yourNormalBamFile.bam /data/yourTumorBamFile.bam /data/winners.hla.txt build format /data

Annotation of mutations

singularity exec -C \
-B /path/to/your/data/directory_with_mutation_detection_output:/data \
-B /path/to/your/temporary/folder:/tmp \
polysolver-singularity_v4.sif /home/polysolver/scripts/shell_annotate_hla_mutations \
prefix /data

Cautions

The Singularity.v4 file only allows to build a Singularity image of Polysolver version 4 coming from the Docker Hub repository of its author.

The methods implemented into Polysolver should not be impacted by our changes.

Singularity version 3.1.1 was used for tests.