{"id":13593297,"url":"https://github.com/robertaboukhalil/ginkgo","last_synced_at":"2025-04-29T11:11:31.976Z","repository":{"id":74654545,"uuid":"9785282","full_name":"robertaboukhalil/ginkgo","owner":"robertaboukhalil","description":"Cloud-based single-cell copy-number variation analysis tool","archived":false,"fork":false,"pushed_at":"2023-03-21T02:12:22.000Z","size":105570,"stargazers_count":49,"open_issues_count":8,"forks_count":29,"subscribers_count":10,"default_branch":"master","last_synced_at":"2025-03-30T12:11:27.394Z","etag":null,"topics":["bioinformatics","sequencing","single-cell-genomics"],"latest_commit_sha":null,"homepage":"qb.cshl.edu/ginkgo","language":"PHP","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/robertaboukhalil.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2013-05-01T03:54:53.000Z","updated_at":"2025-03-06T07:45:02.000Z","dependencies_parsed_at":null,"dependency_job_id":"ff589101-d47d-4654-adc1-6071129e231a","html_url":"https://github.com/robertaboukhalil/ginkgo","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/robertaboukhalil%2Fginkgo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/robertaboukhalil%2Fginkgo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/robertaboukhalil%2Fginkgo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/robertaboukhalil%2Fginkgo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/robertaboukhalil","download_url":"https://codeload.github.com/robertaboukhalil/ginkgo/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251490170,"owners_count":21597564,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","sequencing","single-cell-genomics"],"created_at":"2024-08-01T16:01:18.901Z","updated_at":"2025-04-29T11:11:31.959Z","avatar_url":"https://github.com/robertaboukhalil.png","language":"PHP","readme":"Ginkgo\n=========\n\n#### Ginkgo is a cloud-based single-cell copy-number variation analysis tool.\n#### Launch Ginkgo: [qb.cshl.edu/ginkgo](http://qb.cshl.edu/ginkgo)\n\nUsage\n=========\n\n* Step 0: Upload .bed files\n* Step 1: Choose analysis parameters\n* Step 2: Compute Copy Number Profiles, and a Phylogenetic Tree\n* Step 3: Analyze Individual Cells\n\n\nSetup Ginkgo on your own server\n=========\n\n**Requirements:**\n\n- PHP \u003e=5.2\n- R \u003e= 3.0.0\n- R Packages:\n\t- ctc\n\t- DNAcopy\n\t- inline\n\t- gplots\n\t- scales\n\t- plyr\n\t- ggplot2\n\t- gridExtra\n\t- fastcluster\n\t- heatmap3\n\n**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\n\n```\nremove.packages('gplots'); \nlibrary('devtools'); \ninstall_github(\"ChristophH/gplots\")\n```\n\n\t\n\n**Install Ginkgo:**\n\nType ```make``` in the ginkgo/ directory\n\n**Server Configuration:**\n\n- /etc/php.ini\n\t- ```upload_tmp_dir```: make sure this directory has write permission\n\t- ```upload_max_filesize```: set to \u003e2G since .bam files can be large\n\n- ginkgo/includes/fileupload/server/php/UploadHandler.php\n\t- In constructor, on line 43 and 44:\n\t\t- ```upload_dir = [FULL_PATH_TO_UPLOADS_DIR] . $_SESSION[\"user_id\"] . '/'```\n\t\t- ```upload_url = [FULL_URL_TO_UPLOADS_DIR]  . $_SESSION[\"user_id\"] . '/'```\n\n- ginkgo/bootstrap.php\n\t- Change ```DIR_ROOT```, ```DIR_UPLOADS``` and ```URL_ROOT```\n\n- ginkgo/scripts/analyze.sh\n\t- Change ```home``` variable to where the ginkgo/ folder is located\n\n- ginkgo/scripts/process.R\n\t- Change ```main_dir``` variable to the folder where ginkgo/scripts is located\n\n- ginkgo/scripts/reclust.R\n\t- Change ```main_dir``` variable to the folder where ginkgo/scripts is located\n\n- ginkgo/scripts/analyze-subset.R\n\t- Set the folder to where ginkgo/scripts is located\n\t- Set the folder to where ginkgo/genomes is located (warning: test this carefully if your ginkgo/uploads folder is a symlink)\n\n- Make sure the uploads directory has the correct write permissions\n\n**Download data files:**\n\n- Download binning data for hg19 at https://labshare.cshl.edu/shares/schatzlab/www-data/ginkgo/genomes/hg19.tgz\n\t- untar into ginkgo/genomes/hg19 (which needs to be created)\n\n- 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/\n","funding_links":[],"categories":["Software packages"],"sub_categories":["Copy number analysis"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frobertaboukhalil%2Fginkgo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frobertaboukhalil%2Fginkgo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frobertaboukhalil%2Fginkgo/lists"}