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: Phylogenetic Tree

Step 3: Analyse Individual Cells

Setup Ginkgo on your own server

Requirements:

• PHP >=5.2
• R >=2.15.2
• R Packages:
  • ctc
  • DNAcopy
  • inline
  • gplots
  • scales
  • plyr

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

  • 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