HLA-LOH: Dockerize LOHHLA

[evanbiederstedt]

https://www.ncbi.nlm.nih.gov/pubmed/29107330

https://bitbucket.org/mcgranahanlab/lohhla

HLA LOH

[evanbiederstedt]

People were actually crazy enough to do this before us:

https://hub.docker.com/r/mleventhal/lohhla https://hub.docker.com/r/jingxin/lohhla https://hub.docker.com/r/eszterlakatos/lohhla_conda https://hub.docker.com/r/pici/lohhla

[evanbiederstedt]

Golly, I missed this:

https://quay.io/repository/biocontainers/lohhla?tab=info

docker pull quay.io/biocontainers/lohhla:20171108--1 definitely works

$ docker run -it quay.io/biocontainers/lohhla:20171108--1 /bin/bash
bash-4.2# lohhla                                                               
$HLAfastaLoc
[1] "~/lohhla/data/hla_all.fasta"

$CopyNumLoc
[1] "FALSE"

$overrideDir
[1] "FALSE"

$minCoverageFilter
[1] 30

$kmerSize
[1] 50

$numMisMatch
[1] 1

$mappingStep
[1] TRUE

$fishingStep
[1] TRUE

$plottingStep
[1] TRUE

$coverageStep
[1] TRUE

$cleanUp
[1] TRUE

$novoDir
[1] ""

$gatkDir
[1] ""

$HLAexonLoc
[1] "~/lohhla/data/hla.dat"

$ignoreWarnings
[1] TRUE

$help
[1] FALSE

Usage: /usr/local/bin/lohhla [options]

Options:
    -id CHARACTER, --patientId=CHARACTER
        patient ID

    -o CHARACTER, --outputDir=CHARACTER
        location of output directory

    -nBAM CHARACTER, --normalBAMfile=CHARACTER
        normal BAM file
        can be FALSE to run without normal sample

    -BAM CHARACTER, --BAMDir=CHARACTER
        location of all BAMs to test

    -hla CHARACTER, --hlaPath=CHARACTER
        location to patient HLA calls

    -hlaLoc CHARACTER, --HLAfastaLoc=CHARACTER
        location of HLA FASTA [default= ~/lohhla/data/hla_all.fasta]

    -cn CHARACTER, --CopyNumLoc=CHARACTER
        location to patient purity and ploidy output
        can be FALSE to only estimate allelic imbalance

    -ov CHARACTER, --overrideDir=CHARACTER
        location of flagstat information if already run [default= FALSE]

    -mc CHARACTER, --minCoverageFilter=CHARACTER
        minimum coverage at mismatch site [default= 30]

    -kmer CHARACTER, --kmerSize=CHARACTER
        size of kmers to fish with [default= 50]

    -mm CHARACTER, --numMisMatch=CHARACTER
        number of mismatches allowed in read to map to HLA allele [default= 1]

    -ms CHARACTER, --mappingStep=CHARACTER
        does mapping to HLA alleles need to be done [default= TRUE]

    -fs CHARACTER, --fishingStep=CHARACTER
        if mapping is performed, also look for fished reads matching kmers of size kmerSize [default= TRUE]

    -ps CHARACTER, --plottingStep=CHARACTER
        are plots made [default= TRUE]

    -cs CHARACTER, --coverageStep=CHARACTER
        are coverage differences analyzed [default= TRUE]

    -cu CHARACTER, --cleanUp=CHARACTER
        remove temporary files [default= TRUE]

    -no CHARACTER, --novoDir=CHARACTER
        path to novoalign executable [default= ]

    -ga CHARACTER, --gatkDir=CHARACTER
        path to GATK executable [default= ]

    -ex CHARACTER, --HLAexonLoc=CHARACTER
        HLA exon boundaries for plotting [default= ~/lohhla/data/hla.dat]

    -w CHARACTER, --ignoreWarnings=CHARACTER
        continue running with warnings [default= TRUE]

    -h, --help
        Show this help message and exit

Error: Missing arguments.
Execution halted
bash-4.2#