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Ginkgo

Ginkgo is a cloud-based single-cell copy-number variation analysis tool.

Launch Ginkgo: qb.cshl.edu/ginkgo

Usage

  • Step 0: Upload .bed files
  • Step 1: Choose analysis parameters
  • Step 2: Compute Copy Number Profiles, and a Phylogenetic Tree
  • Step 3: Analyze Individual Cells

Setup Ginkgo on your own server

Requirements:

  • PHP >=5.2
  • R >= 3.0.0
  • R Packages:
    • ctc
    • DNAcopy
    • inline
    • gplots
    • scales
    • plyr
    • ggplot2
    • gridExtra
    • fastcluster
    • heatmap3

WARNING Version 3.0.0 (Mar 28, 2016) of gplots introduced a bug in heatmap.2 that makes it calculate dendrograms even when Rowv or Colv is set to FALSE so that Ginkgo will run for a very long time. The solution is to use an older version of gplots or use fixed version from: https://github.com/ChristophH/gplots. This can be installed using the commands below

remove.packages('gplots'); 
library('devtools'); 
install_github("ChristophH/gplots")

Install Ginkgo:

Type make in the ginkgo/ directory

Server Configuration:

  • /etc/php.ini

    • upload_tmp_dir: make sure this directory has write permission
    • upload_max_filesize: set to >2G since .bam files can be large

  • ginkgo/includes/fileupload/server/php/UploadHandler.php

    • In constructor, on line 43 and 44:
      • upload_dir = [FULL_PATH_TO_UPLOADS_DIR] . $_SESSION["user_id"] . '/'
      • upload_url = [FULL_URL_TO_UPLOADS_DIR] . $_SESSION["user_id"] . '/'

  • ginkgo/bootstrap.php

    • Change DIR_ROOT, DIR_UPLOADS and URL_ROOT

  • ginkgo/scripts/analyze.sh

    • Change home variable to where the ginkgo/ folder is located

  • ginkgo/scripts/process.R

    • Change main_dir variable to the folder where ginkgo/scripts is located

  • ginkgo/scripts/reclust.R

    • Change main_dir variable to the folder where ginkgo/scripts is located

  • ginkgo/scripts/analyze-subset.R

    • Set the folder to where ginkgo/scripts is located
    • Set the folder to where ginkgo/genomes is located (warning: test this carefully if your ginkgo/uploads folder is a symlink)

  • Make sure the uploads directory has the correct write permissions

Download data files: