Practical Haplotype Graph Docker Implementation Example Config File

Question

[CLOE.POGODA]

Using the docker implementation, I have successfully run the test example. However, when I get to step 1.B and run:

WORKING_DIR=local/directory/where/MakeDefaultDirectory/was/run/
DOCKER_CONFIG_FILE=/phg/config.txt
docker run --name create_initial_db --rm \
    -v ${WORKING_DIR}/:/phg/ \
    -t maizegenetics/phg:latest \
    /tassel-5-standalone/run_pipeline.pl -Xmx100G -debug -configParameters ${DOCKER_CONFIG_FILE} \
    -MakeInitialPHGDBPipelinePlugin -endPlugin

I get the following error:

Exception in thread "main" java.lang.IllegalArgumentException: TasselPipeline: main: -configParameters file: -CreateValidIntervalsFilePlugin doesn't exist or isn't a file.
        at net.maizegenetics.pipeline.TasselPipeline.main(TasselPipeline.java:306)

This indicates to me that I need to assign values for the currently UNASSIGNED variables. However, I cannot find any documentation or examples of the config file. Is it possible to receive an example config.txt so I can modify my file as necessary? Thanks.

Answer 1

[zrm22]

Hello, yes you need to set any parameter marked as UNASSIGNED. If you delete the current UNASSIGNED values and add the following(and update them to reflect what you have), it should work better. I will update the wiki to have an example with these changes.

#General Graph Building parameters
#Should depend on either asmMethod, LoadHaplotypesFromGVCFPlugin.haplotypeMethodName or RunHapConsensusPipelinePlugin.collapseMethod depending on what you are running.
HaplotypeGraphBuilderPlugin.methods=mummer4

LoadAllIntervalsToPHGdbPlugin.genomeData=/phg/inputDir/reference/Ref_Assembly_load_data.txt
LoadAllIntervalsToPHGdbPlugin.outputDir=/phg/outputDir/align/
LoadAllIntervalsToPHGdbPlugin.anchors=/phg/anchors.bed

#These two need to match. And the Ref.fa should be replaced with your reference.
referenceFasta=/phg/inputDir/reference/Ref.fa
LoadAllIntervalsToPHGdbPlugin.ref=/phg/inputDir/reference/Ref.fa

#Loading WGS Haplotype Parameters.
LoadHaplotypesFromGVCFPlugin.wgsKeyFile=/phg/keyFile.txt

## This should be assigned an informative method name to be loaded into the db.  
#It should represent the samples and types of data creating the haplotypes.
LoadHaplotypesFromGVCFPlugin.haplotypeMethodName=GATK_PIPELINE
LoadHaplotypesFromGVCFPlugin.gvcfDir=/phg/inputDir/loadDB/gvcf/

#Set this if you want to store a different name
RunHapConsensusPipelinePlugin.collapseMethod=CONSENSUS

AssemblyHaplotypesMultiThreadPlugin.outputDir=/phg/outputDir/align/
AssemblyHaplotypesMultiThreadPlugin.keyFile=/phg/asm_keyFile.txt

If you are doing assemblies, HaplotypeGraphBuilderPlugin.methods should be set to mummer4. If using GVCFs, it should match whatever is set by LoadHaplotypesFromGVCFPlugin.haplotypeMethodName.