InstanceType

For ArrayServer with Cloud configuration, set any InstanceType for each analysis. By default it is using OAlignInstanceType and OSummaryInstanceType set in ArrayServer.cfg

Example with c4.2xlarge but user can choose other instance too:

Begin RnaSeqPipeline /Namespace=NgsLib /RunOnServer=True;
Files
"/CloudFolderEast/_FASTQ/RNASEQ/Test200PE_1.fastq.gz
/CloudFolderEast/_FASTQ/RNASEQ/Test200PE_2.fastq.gz
/CloudFolderEast/_FASTQ/RNASEQ/Test400PE_1.fastq.gz
/CloudFolderEast/_FASTQ/RNASEQ/Test400PE_2.fastq.gz";
Reference Human.B37.3;
GeneModel OmicsoftGene20130723;
NgsQCWizard /Run=True;
FilterNgsFiles /Run=True;
FilterSource IlluminaAdapters,Ercc,Human.rRNA,Human.tRNA;
Count /Run=True /AutoTrimUtr=False;
RnaSeqQCMetrics /Run=True;
SummarizeExonJunction /Run=True;
SummarizeMutation2Snp /Run=True;
CombinedFusionAnalysis /Run=True;
PairedEndFusionAnalysis /Run=True;
GenerateBas /Run=True;
GenerateLandAlv /Run=True;
Options /ParallelJobNumber=50 /ThreadNumberPerJob=4 /PairedEnd=True /FileFormat=AUTO 
/OutputFolder="/CloudFolderEast/_Users/gary/Test/Test0721" /CompressionMethod=Gzip /Gzip=True 
/Replace=False /SubnetID=subnet-b569b9c2 /InstanceType=c4.2xlarge;
Output TestOthers;
End;

WARNING: Although quoting the string value usually works (e.g. /InstanceType="c4.2xlarge"), in some procedures (e.g. MapRnaSeqReadsToGenome), the quotes are not removed when the Options statement is parsed which causes failure - see "Instance Creation is not successful" error

Also Read

• OAlignInstanceType
• OSummaryInstanceType
• "Instance Creation is not successful" error