ArrayLand Configuration Options

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Contents

Configuration file

Multiple Lands can be hosted on ArrayServer.

Land options can be configured in ArrayServer.cfg, where each land is configured with a [land] section.

However, it is recommended to host Lands in LandDirectory, with one folder for each land (folder name is LandName).

Customizing Land Configurations (LandName.cfg2)

In each folder, a LandName.cfg file inside the land folder is used for default configuration of individual Lands. 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


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

And each directory will have a file for Land-specific configuration options:

Server CCLEcfg.png

User

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 ""
SubscribedSampleSets N ""
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 10000 (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

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