ArrayLand Configuration Options

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[Category: Updated in 2017]

Contents

Configuration file

Multiple Lands can be hosted on ArrayServer. The land data is stored within the LandDirectory that is specified in the ArrayServer.cfg.

For example, if ArrayServer.cfg contains the line

LandDirectory=/mnt/Scratch/ArrayServer/LandDir/Test-08_LandDir

This directory will contain a series of subdirectories, one for each Land:

Server LandDirectories.png

Customizing Land Configurations (LandName.cfg2)

Land options can be configured in ArrayServer.cfg. However, we strongly recommend using the LandName.cfg file inside the land sub-directory for default configuration of individual Lands.

Server CCLEcfg.png

Additional user configurations can also be added into a LandName.cfg2 file. Any parameters set in LandName.cfg2 will overwrite parameters in LandName.cfg.

Tips.png

Cloud-based Lands automatically over-write LandName.cfg in your Server's Land directory with every update. Be sure to place all customizations in LandName.cfg2


Configuration Options

Parameter Required Default
Name Y .
Version N 3
Description N No description
Folder Y Only required if used in ArrayServer.cfg; not used in LandName.cfg
ReferenceLibraryID Y .
GeneModelID Y .
MutationGeneModelID Y .
SubjectIDColumn N SubjectID
SampleTypeColumn N Sample Type
ControlSampleLevels N Blood Derived Normal, Solid Tissue Normal, Bone Marrow Normal
AutoFilterColumn N Same as PrimaryGrouping
AutoFilterLabel N AutoFilterColumn column name
AutoFilterOffGrouping N Tumor Type
AutoFilterOnGrouping N Sample Type
PrimaryGrouping N Same as AutoFilterOffGrouping
SecondaryGrouping N Same as AutoFilterOnGrouping
PrimaryProjectGrouping N TherapeuticArea
PrimaryAssociationGrouping N
SecondaryAssociationGrouping N
AutomaticGrouping N Same as PrimaryGrouping
EnableBam N FALSE
EnableBas N FALSE
BamFolder N ""
BasFolder N ""
DnaSeqTargetBamFolder N ""
DnaSeqTargetBasFolder N ""
DnaSeqBamFolder N ""
DnaSeqBasFolder N ""
DnaSeqExomeBamFolder N ""
DnaSeqExomeBasFolder N ""
SingleEndFusionBamFolder N ""
PairedEndFusionBamFolder N ""
SingleEndFusionBasFolder N ""
PairedEndFusionBasFolder N ""
VirusBamFolder N ""
VirusBasFolder N ""
MicrobesBamFolder N ""
MicrobesBasFolder N ""
FunctionalAnnotationFiles N ""
VariantClassifiers N ""
CosmicFile N ""
DbsnpVersion N Dbsnp138 for Human and Dbsnp137 for Mouse before 2015 Q2
ClinicalHistogramViewColumns N PrimaryGrouping,SecondaryGrouping
CnvAmplificationCutoff N 3
CnvDeletionCutoff N 1
ExpressionUpRegulationCutoff N 1
ExpressionDownRegulationCutoff N -1
SurvivalTimeColumn N Survival Days
SurvivalStatusColumn N Survival Status
SurvivalDeathStatus N DECEASED
MaxGeneCount N 500
MaxSampleCount N 2000
MaxMeasurementCount N 10000
HomePage N ""
IsReadOnly|N FALSE
MinimalSeedFusionCutoff N ""
OrganizeBamByPrimaryGrouping N ""
OrganizeBasByPrimaryGrouping N ""
OrganizeFusionBamByPrimaryGrouping N ""
OrganizeFusionBasByPrimaryGrouping N ""
IntegrationLevel N ""
SEFusionCutoff N 3
PEFusionCutoff N 4
MinimalExonJunctionCutoff N 5
DefaultViewID.ContextType N Explicitly set the default view for the specified Land context, such as Default,Gene,ComparisonSet, etc.
DefaultViewID.Default N explicitly set the default view for each land context, such as "LandHomePage"
DefaultViewID.Gene N explicitly set the default view to be a gene for each land context
EnableLandNumericCache N False
CollectionName N A name you like
CNVCallingMethod N Select the Default Copy Number Calling Method, when both are available
TopHitsN N 2000 (also the minimum if a lower value is configured)
MaxTopHitsN N 500000 (also the minimum if a lower value is configured)
DefaultProjectAccess N [usergroup]administrators,[usergroup]standard users
DefaultProjectFrequencyAccess N [usergroup]administrators,[usergroup]standard users
AdminEmail N
MandatoryAssociationMetaDataColumns N
MandatorySampleMetaDataColumns N

Example of Land Configuration

Example in ArrayServer.cfg

[Folder]
BAMFile=/IData/BAM
BASFile=/IData/BAS
ArrayLand=/IData/ArrayLand
[Land]
Name=TCGA
Folder=/IData/ArrayLand/TCGA
ReferenceLibraryID=Human.B37.3
GeneModelID=UcscGene20120907
AutoFilterColumn=Tumor Type
AutoFilterLabel=Tumor Type
AutoFilterOffGrouping=Tumor Type
AutoFilterOnGrouping=Sample Type
BamFolder=/BAMFile/bamfile
BasFolder=/BASFile/Bas
EnableBas=True
EnableBam=True
SingleEndFusionBamFolder=/BAMFile/FusionBamSE
PairedEndFusionBamFolder=/BAMFile/FusionBamPE
SingleEndFusionBasFolder=/BASFile/FusionBasSE
PairedEndFusionBasFolder=/BASFile/FusionBasPE
FunctionalAnnotationFiles=Human.B37.3_FunctionalMutation20130408.gbt,Human.B37.3_CosmicMutation_V64.gbt,Human.B37.3_1000Genome_2011_0521.compact.gbt
MaxGeneCount=500
HomePage=http://www.omicsoft.com/TCGA-Land.html

Example in CompanyLand.cfg

Name=CompanyLand_B37
ReferenceLibraryID=Human.B37.3
GeneModelID=OmicsoftGene20130723
PrimaryGrouping=Tumor Type
SecondaryGrouping=Sample Type
FunctionalAnnotationFiles=Human.B37.3_FunctionalMutation20150406.gbt,Human.B37.3_CosmicMutation_V70.gbt,Human.B37.3_1000Genome_2013_0502.compact.gbt,OT:ucscGenePfam
VariantClassifiers=ClinVar_20160115,FunctionalMutation_20160115,1000GenomesSimple_20160115,ExAC_20160115,ESP6500_20160115,UK10K_20160115,GTExEqtl_20160115,RegulomeDB_20160115,Interpro_20160115
MutationGeneModelID=Uniprot.Ensembl75
Description=Company Internal Land Description
MaxGeneCount=500
MinimalSeedFusionCutoff=3
EnableLandNumericCache=True
EnableLandAnalysisCache=True
Version=3

EnableBam=True
BamFolder=/ArrayServer/CompanyLand/bam
EnableBas=True
BasFolder=/ArrayServer/CompanyLand/bam
SingleEndFusionBamFolder=/ArrayServer/CompanyLand/alv/SingleEndFusionBam
SingleEndFusionBasFolder=/ArrayServer/CompanyLand/alv/SingleEndFusionBas
PairedEndFusionBamFolder=/ArrayServer/CompanyLand/alv/PairedEndFusionBam
PairedEndFusionBasFolder=/ArrayServer/CompanyLand/alv/PairedEndFusionBas

Example GeneticsLand.cfg

Description=GeneticsLandTutorial
GeneModelID=OmicsoftGene20130723
IsGeneticsLand=True
MaxGeneCount=500
MutationGeneModelID=Uniprot.Ensembl75
Name=Tutorial
PrimaryAssociationGrouping=StudyID
PrimaryGrouping=ProjectName
ReferenceLibraryID=Human.B37.3
SecondaryAssociationGrouping=TraitCategory
SecondaryGrouping=Sex
SubjectIDColumn=USUBJID
VariantClassifiers=ClinVar_20160115,FunctionalMutation_20160115,1000GenomesSimple_20160115
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