Goal
Enable customers to run STAR on multiple fastq samples in parallel, on server, HPC, or AWS Cloud, resulting in a pair of OmicData objects in an OmicSoft Suite project.
Customer Workflow (via escript)
The above examples contain a fully functional flow on STAR alignment flow, on cloud, with docker.
The following environment preconditions have been set:
- AMI with docker V19.03.8: ami-012cb9a6d92521948
- Docker Image (Docker images don't require prerequisites)
A complete STAR flow requires the following steps:
Build index
Preconditions:
- InstanceType: m4.4xlarge
- Additional Volume: 100GB
| STAR Index
|
Begin Macro;
@NSLOTS@ 20;
@readlength@ 100;
End;
Begin RunEScript /RunOnServer=True;
Resources
"/VirtualCloudFolder/ArrayServer/Input/gencode.v33.annotation.gtf";
Files "/VirtualCloudFolder/ArrayServer/Input/GRCh38.p13.genome.fa";
EScriptName StarTest;
Command STAR --runThreadN @NSLOTS@ --runMode genomeGenerate --genomeDir %OutputFolder% --genomeFastaFiles %FilePath% --sjdbGTFfile %Resource1% --sjdbOverhang @readlength@;
Options /ParallelJobNumber=1 /ThreadNumberPerJob=8 /Mode=Single /ErrorOnStdErr=False /ErrorOnMissingOutput=True /RunOnDocker=True /ImageName="quay.io/biocontainers/star:2.7.3a--0" /UseCloud=True /UseDev2=True /OutputFolder="/VirtualCloudFolder/Output/Results/StarIndex" /InstanceType=m4.4xlarge /VolumeSize=100;
End;
|
