Running_Helium_Datacommons.md

Running in Helium Datacommons

This document describes running the TOPMed RNA-seq pipeline in the Helium DataCommons environment.

Steps:

• Register files into iRODS
  • STAR index
  • RSEM reference
  • Genome FASTA
  • Genes GTF
  • Unpack tar and gz files.

  $ cd /renci/irods/topmed-demo/
  $ gunzip -c LC_C13_cRNA_sequence_R1.txt.gz > LC_C13_cRNA_sequence_R1.fastq
  $ gunzip -c LC_C13_cRNA_sequence_R2.txt.gz > LC_C13_cRNA_sequence_R2.fastq
  $ mkdir star_index
  $ tar -xvvf STAR_genome_GRCh38_noALT_noHLA_noDecoy_ERCC_v26_oh100.tar.gz -C star_index --strip-components=1
  

  • Run ireg command for all files into desired resource.
• Start an appliance using the instructions here.
• Run with toil

cwltoil --noLinkImports --jobStore /<path>/jobstore1 --batchSystem chronos --workDir ./ /<path>/<workflow>.cwl /<path>/<workflow-inputs>.yml