DarcyMyers / nci-workshop

Repository for the NCI Cloud Pilot Workshop on May 24-25, 2016

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#NCI Cloud Pilot Workshop - May 24-25, 2016

Overview

####This project contains these tools and workflows:

  • sonnet-grep (tool)
  • dna2protein (workflow)
    • transcribe (tool)
    • translate (tool)
  • GeneExpressionWF (workflow)
    • Gene Expression Munger (tool)
    • Differential Expression (tool)

##sonnet-grep This tool looks for patterns in a text file (Shakespeare's 18th Sonnet) and outputs the lines that match. grep is a standard Linux command line tool.

##dna2protein This workflow takes a input text file with a DNA sequence and outputs a text file with a peptide sequence from the first ORF, if possible. dna2protein is a custom workflow written in Python that is composed of transcribe.py (DNA -> mRNA) and translate.py (mRNA -> protein).

##GeneExpressionWF This workflow produces a differential expression analysis from an array of Level 3 TCGA RNASeq Gene Expression Quantification files. It first merges the files into a single matrix and produces a "metadata matrix" from the metadata (e.g. sample type, gender) from each individual case (GeneExpressionMunger, munger.py). It then runs a custom differential expression analysis that produces a matrix of (adj) p-values per gene based on differences among sample-types (e.g. Solid Tissue Normal and Primary Tumor) as well as some plots in PDF (DifferentialExpression, diff.R).

##Import tools from this repository into a CGC project You can import any CWL JSON in these projects as a tool into the Cancer Genomics Cloud. First, you must set up a CGC account and create a project.

Steps:

  1. In a project on the CGC, navigate to the Apps tab, then 'Add App'

  2. Input a name for your app: alt-tag

  3. In the Tool Editor, click on '...' on the upper-right and then select 'Import': alt-tag

  4. You will see a blank window. Paste the contents of the CWL JSON file (*.cwl.json) from this repo: alt-tag alt-tag

  5. Click 'Import'. You will see the appropriate fields in the Tool Editor window: alt-tag

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Repository for the NCI Cloud Pilot Workshop on May 24-25, 2016


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