{"id":18586299,"url":"https://github.com/mayurdivate/guavasourcecode","last_synced_at":"2025-05-16T06:34:24.474Z","repository":{"id":53874653,"uuid":"102445953","full_name":"MayurDivate/GUAVASourceCode","owner":"MayurDivate","description":"Source code repository for GUAVA (ATAC-seq data analysis tool).","archived":false,"fork":false,"pushed_at":"2021-05-20T23:52:13.000Z","size":29596,"stargazers_count":3,"open_issues_count":19,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2024-12-26T18:23:46.298Z","etag":null,"topics":["atac-seq","bioinformatics","guava","pipeline","tool"],"latest_commit_sha":null,"homepage":"","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MayurDivate.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}},"created_at":"2017-09-05T07:00:20.000Z","updated_at":"2021-05-20T23:52:15.000Z","dependencies_parsed_at":"2022-09-05T01:40:15.983Z","dependency_job_id":null,"html_url":"https://github.com/MayurDivate/GUAVASourceCode","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/MayurDivate%2FGUAVASourceCode","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MayurDivate%2FGUAVASourceCode/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MayurDivate%2FGUAVASourceCode/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MayurDivate%2FGUAVASourceCode/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MayurDivate","download_url":"https://codeload.github.com/MayurDivate/GUAVASourceCode/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239340504,"owners_count":19622704,"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":["atac-seq","bioinformatics","guava","pipeline","tool"],"created_at":"2024-11-07T00:37:47.549Z","updated_at":"2025-02-17T17:56:15.860Z","avatar_url":"https://github.com/MayurDivate.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"# GUAVA : A GUI tool for the Analysis and Visualization of ATAC-seq data\n[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://github.com/MayurDivate/GUAVASourceCode/blob/master/LICENSE) \n[![OS: mac | linux](https://img.shields.io/badge/OS-mac%20%7C%20linux-red.svg)](https://github.com/MayurDivate/GUAVASourceCode#guava--a-gui-tool-for-the-analysis-and-visualization-of-atac-seq-data) \n[![institute](https://img.shields.io/badge/Institute-University%20of%20Macau-blue.svg)](http://www.umac.mo)\n\n\u003cp align=\"justify\"\u003eIn nutshell, GUAVA is a standalone GUI tool for processing, analyzing and visualizing ATAC-seq data. A user can start GUAVA analysis with raw reads to identify ATAC-seq signals. Then ATAC-seq signals from two or more samples can be compared using GUAVA to identify genomic loci with differentially enriched ATAC-seq signals. Furthermore, GUAVA also provides gene ontology and pathways enrichment analysis. Since to use GUAVA requires only several clicks and no learning curve, it will help novice bioinformatics researchers and biologist with minimal computer skills to analyze ATAC-seq data. Therefore, we believe that GUAVA is a powerful and time saving tool for ATAC-seq data analysis. GUAVA setup contains a script to configure and install dependencies which facilitates the GUAVA installation. GUAVA works on Linux and Mac OS.\u003c/p\u003e\n\n\u003e GUAVA is developed in the Edwin’s laboratory at University of Macau.\n\n## Quick Start\n## Download\nFirst download the GUAVA package.\u003cbr/\u003e\n\u003cbr/\u003e\nStep 1: Go to the [**link**](https://github.com/MayurDivate/GUAVA/releases) \u003cbr/\u003e\nStep 2: Click on the `Source Code (zip)` \u003cbr/\u003e\nStep 3: This will save GUAVA zip package in the downloads folder \u003cbr/\u003e\n\u003cbr/\u003e\nThen you will need to open the terminal to complete installation.\u003cbr/\u003e\nPlease check the [**manual**](http://ec2-52-201-246-161.compute-1.amazonaws.com/guava/docs/GUAVA_manual.pdf) to know how to open the terminal.\u003cbr/\u003e\n\u003cbr/\u003e\nIf the downloaded package is in the folder ```Downloads```,Then type the commands below to unzip package on the terminal.\u003cbr/\u003e\n\n```\nmv ~/Downloads/GUAVA-1.zip ~/\ncd ~/\nunzip GUAVA-1.zip\n```\n\nNOTE: If you have downloaded and saved GUAVA package in any other folder that Downloads. You will have to use complete path of that folder in above command instead of `~/Downloads/GUAVA-master.zip`. To copy path, simply copy the downloaded package and paste it on the terminal. \n\n## Installing Dependencies\nThough we have written configure.sh script for the easy installation of dependencies, R and MACS2 need to be installed manually.\n\u003cbr/\u003e\n\n## 1 INSTALL R \n#MAC \nStep 1: Download R =\u003e [**Click Here**](https://cran.r-project.org/bin/macosx/) \u003cbr/\u003e\nStep 2: Click on the R-X.X.X.pkg file link (e.g. R-3.4.3.pkg) \u003cbr/\u003e\nStep 3: Double click on the downloaded R package \u003cbr/\u003e\nStep 4: This will open a R installation window \u003cbr/\u003e\nStep 5: Click on the `continue` and follow the instructions on the screen \u003cbr/\u003e\nStep 6: After the successful installation of R proceed to next section \u003cbr/\u003e\n\n#Linux\nStep 1: Open the terminal \u003cbr/\u003e\nStep 2: Type command ` sudo apt-get install r-base` and press enter \u003cbr/\u003e\n\nTo know more about it, open the [**link**](https://cran.r-project.org/bin/linux/). Then, choose appropriate Linux OS type.\n\n## 2 Install other dependencies and R packages\nStep 1: Open the terminal \u003cbr/\u003e\nStep 2: Use following commands to run configure.sh. \u003cbr/\u003e\nNote: This may take a while to finish. Also, you will need to press ‘enter’ several times\nto continue. Additionally, answer all question with ‘yes’.\n\n```\ncd ~/\nsh ./configure.sh \n```\n[**Anaconda Error**](https://github.com/MayurDivate/GUAVA#anaconda-error-missing-write-permissions-in)\n\n## 3 Install MACS2\nStep 1: Open the terminal \u003cbr/\u003e\nStep 2: And use following commands \u003cbr/\u003e\nNOTE: If permission denied, type 'sudo' at the beginning of the commands.\nThen, to continue installation you have enter your password.\n\nwithout sudo | with sudo\n-----------|------------\n``` cd ~/GUAVA-1 ``` | ``` cd ~/GUAVA-1 ```  \n``` python get-pip.py ``` | ``` sudo python get-pip.py ```\n``` pip install MACS2 ``` | ``` sudo pip install MACS2 ```\n\nEnd of the installation part.\n\u003cbr/\u003e\n## To start GUAVA use following command\n\n**GUI version**\n```\n java -jar GUAVA.jar\n```\n**For command line interface**\n```\n java -jar GUAVA.jar [options]*\n```\n\n## GUAVA manual\n[**click here**](http://ec2-52-201-246-161.compute-1.amazonaws.com/guava/docs/GUAVA_manual.pdf)\n\n\n## Sample Data\nTo download sample data [ **Click Here** ](https://drive.google.com/drive/folders/1TqSOOAuA6wRJVCeOMTD8q7RE1fscAoe2?usp=sharing)\n\n## Anaconda Error: Missing write permissions in\nIf you encounter error which says \"Error: Missing write permissions in:/share/apps/anaconda***\",\u003cbr/\u003e\nplease follow the commands below to create local Anaconda enviroment.  \n\n- Use the command below and replace the text after 'clone=' with your Anaconda path. Check the error to know correct path. \n```\nconda create -n my_root --clone=/share/apps/anaconda2/4.0.0\n``` \n- use commands below to activate loacal my_root anaconda\n```\nsource activate my_root\nconda remove conda-build\nconda remove conda-env\nconda update anaconda\n```\n- try to install dependencies again\n``\ncd ~/GUAVA-1\nsh ./configure.sh\n``\n\n## System Requirements\n- Java 1.8 or latest\n- Python version 2.7\n- R Version: \u003e= 3.3.2\u003cbr/\u003e\n\n## Required bioinformatics tools\n- Bowtie\n- Bowtie2\n- MACS2 version 2.1.1.20160309\n- SAMtools Version: 1.3.1\n- FastQC\n- cutadapt\n- bedtools\n- bedGraphToBigWig\n\n### List of required R Packages\n- ChIPseeker\n- DESeq2\n- ReactomePA\n- TxDb.Hsapiens.UCSC.hg19.knownGene\n- TxDb.Mmusculus.UCSC.mm9.knownGene\n- TxDb.Mmusculus.UCSC.mm10.knownGene\n- org.Hs.eg.db\n- org.Mm.eg.db\n- ChIPpeakAnno\n- GO.db\n- KEGG.db\n- EnsDb.Hsapiens.v75\n- Rsubread\n- ggplot2\n\n## Support\n If you're having any problem, please [raise an issue](https://github.com/MayurDivate/GUAVASourceCode/issues) on GitHub. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmayurdivate%2Fguavasourcecode","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmayurdivate%2Fguavasourcecode","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmayurdivate%2Fguavasourcecode/lists"}