https://github.com/mayurdivate/guavasourcecode
Source code repository for GUAVA (ATAC-seq data analysis tool).
https://github.com/mayurdivate/guavasourcecode
atac-seq bioinformatics guava pipeline tool
Last synced: 5 months ago
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Source code repository for GUAVA (ATAC-seq data analysis tool).
- Host: GitHub
- URL: https://github.com/mayurdivate/guavasourcecode
- Owner: MayurDivate
- License: gpl-3.0
- Created: 2017-09-05T07:00:20.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2021-05-20T23:52:13.000Z (over 4 years ago)
- Last Synced: 2024-12-26T18:23:46.298Z (10 months ago)
- Topics: atac-seq, bioinformatics, guava, pipeline, tool
- Language: Java
- Homepage:
- Size: 28.2 MB
- Stars: 3
- Watchers: 4
- Forks: 0
- Open Issues: 19
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# GUAVA : A GUI tool for the Analysis and Visualization of ATAC-seq data
[](https://github.com/MayurDivate/GUAVASourceCode/blob/master/LICENSE)
[](https://github.com/MayurDivate/GUAVASourceCode#guava--a-gui-tool-for-the-analysis-and-visualization-of-atac-seq-data)
[](http://www.umac.mo)
In 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.
> GUAVA is developed in the Edwin’s laboratory at University of Macau.
## Quick Start
## Download
First download the GUAVA package.
Step 1: Go to the [**link**](https://github.com/MayurDivate/GUAVA/releases)
Step 2: Click on the `Source Code (zip)`
Step 3: This will save GUAVA zip package in the downloads folder
Then you will need to open the terminal to complete installation.
Please 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.
If the downloaded package is in the folder ```Downloads```,Then type the commands below to unzip package on the terminal.
```
mv ~/Downloads/GUAVA-1.zip ~/
cd ~/
unzip GUAVA-1.zip
```
NOTE: 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.
## Installing Dependencies
Though we have written configure.sh script for the easy installation of dependencies, R and MACS2 need to be installed manually.
## 1 INSTALL R
#MAC
Step 1: Download R => [**Click Here**](https://cran.r-project.org/bin/macosx/)
Step 2: Click on the R-X.X.X.pkg file link (e.g. R-3.4.3.pkg)
Step 3: Double click on the downloaded R package
Step 4: This will open a R installation window
Step 5: Click on the `continue` and follow the instructions on the screen
Step 6: After the successful installation of R proceed to next section
#Linux
Step 1: Open the terminal
Step 2: Type command ` sudo apt-get install r-base` and press enter
To know more about it, open the [**link**](https://cran.r-project.org/bin/linux/). Then, choose appropriate Linux OS type.
## 2 Install other dependencies and R packages
Step 1: Open the terminal
Step 2: Use following commands to run configure.sh.
Note: This may take a while to finish. Also, you will need to press ‘enter’ several times
to continue. Additionally, answer all question with ‘yes’.
```
cd ~/
sh ./configure.sh
```
[**Anaconda Error**](https://github.com/MayurDivate/GUAVA#anaconda-error-missing-write-permissions-in)
## 3 Install MACS2
Step 1: Open the terminal
Step 2: And use following commands
NOTE: If permission denied, type 'sudo' at the beginning of the commands.
Then, to continue installation you have enter your password.
without sudo | with sudo
-----------|------------
``` cd ~/GUAVA-1 ``` | ``` cd ~/GUAVA-1 ```
``` python get-pip.py ``` | ``` sudo python get-pip.py ```
``` pip install MACS2 ``` | ``` sudo pip install MACS2 ```
End of the installation part.
## To start GUAVA use following command
**GUI version**
```
java -jar GUAVA.jar
```
**For command line interface**
```
java -jar GUAVA.jar [options]*
```
## GUAVA manual
[**click here**](http://ec2-52-201-246-161.compute-1.amazonaws.com/guava/docs/GUAVA_manual.pdf)
## Sample Data
To download sample data [ **Click Here** ](https://drive.google.com/drive/folders/1TqSOOAuA6wRJVCeOMTD8q7RE1fscAoe2?usp=sharing)
## Anaconda Error: Missing write permissions in
If you encounter error which says "Error: Missing write permissions in:/share/apps/anaconda***",
please follow the commands below to create local Anaconda enviroment.
- Use the command below and replace the text after 'clone=' with your Anaconda path. Check the error to know correct path.
```
conda create -n my_root --clone=/share/apps/anaconda2/4.0.0
```
- use commands below to activate loacal my_root anaconda
```
source activate my_root
conda remove conda-build
conda remove conda-env
conda update anaconda
```
- try to install dependencies again
``
cd ~/GUAVA-1
sh ./configure.sh
``
## System Requirements
- Java 1.8 or latest
- Python version 2.7
- R Version: >= 3.3.2
## Required bioinformatics tools
- Bowtie
- Bowtie2
- MACS2 version 2.1.1.20160309
- SAMtools Version: 1.3.1
- FastQC
- cutadapt
- bedtools
- bedGraphToBigWig
### List of required R Packages
- ChIPseeker
- DESeq2
- ReactomePA
- TxDb.Hsapiens.UCSC.hg19.knownGene
- TxDb.Mmusculus.UCSC.mm9.knownGene
- TxDb.Mmusculus.UCSC.mm10.knownGene
- org.Hs.eg.db
- org.Mm.eg.db
- ChIPpeakAnno
- GO.db
- KEGG.db
- EnsDb.Hsapiens.v75
- Rsubread
- ggplot2
## Support
If you're having any problem, please [raise an issue](https://github.com/MayurDivate/GUAVASourceCode/issues) on GitHub.