/ginkgo

Cloud-based single-cell copy-number variation analysis tool

Primary LanguageJavaScript

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