Requirements:
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 permissionupload_max_filesize
: set to >2G since .bam files can be largeginkgo/includes/fileupload/server/php/UploadHandler.php
upload_dir = [FULL_PATH_TO_UPLOADS_DIR] . $_SESSION["user_id"] . '/'
upload_url = [FULL_URL_TO_UPLOADS_DIR] . $_SESSION["user_id"] . '/'
ginkgo/bootstrap.php
DIR_ROOT
, DIR_UPLOADS
and URL_ROOT
ginkgo/scripts/analyze.sh
home
variable to where the ginkgo/ folder is locatedginkgo/scripts/process.R
main_dir
variable to the folder where ginkgo/scripts is locatedginkgo/scripts/reclust.R
main_dir
variable to the folder where ginkgo/scripts is locatedginkgo/scripts/analyze-subset.R
Make sure the uploads directory has the correct write permissions
Download data files:
Download binning data for hg19 at https://labshare.cshl.edu/shares/schatzlab/www-data/ginkgo/genomes/hg19.tgz
Other genomes, including hg18, hg19, mm9, mm10, rheMac7, rheMac8, rn5 and dm3 can be found at http://labshare.cshl.edu/shares/schatzlab/www-data/ginkgo/genomes/