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Update README.md to use biocontainers' containers #125

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Update README.md to use biocontainers' containers #125

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Update README.md to use biocontainers' containers
eburgueno Oct 18, 2020
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oushujun Dec 1, 2020
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38 changes: 23 additions & 15 deletions README.md
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Expand Up @@ -7,9 +7,9 @@

* [Introduction](#introduction)
* [Installation](#installation)
* [Quick installation using conda](#quick-installation-using-conda)
* [Quick installation using conda](#quick-installation-using-conda-linux64)
* [Quick installation using Singularity](#quick-installation-using-singularity-good-for-hpc-users)
* [Quick installation using Docker](#quick-installation-using-docker-good-for-root-users)
* [Quick installation using Docker](#quick-installation-using-docker-good-for-root-mac-users)
* [Step by step installation using conda ](#step-by-step-installation-using-conda)
* [Testing](#testing)
* [Inputs](#inputs)
Expand Down Expand Up @@ -39,35 +39,43 @@ For benchmarking of a testing TE library, I have provided the curated TE annotat
There are four ways to install EDTA. Please choose one.

### Quick installation using conda (Linux64)
conda install -c bioconda edta

`conda install -c bioconda -c conda-forge edta`


### Quick installation using [Singularity](https://sylabs.io/docs/) (good for HPC users)
Installation:

singularity build --sandbox EDTA.sif docker://kapeel/edta
`singularity pull EDTA.sif docker://quay.io/biocontainers/edta:<tag>`

Visit [BioContainers' Quay.io](https://quay.io/repository/biocontainers/edta?tab=tags) repository for a list of available tags.

Usage:

singularity exec {path}/EDTA.sif /EDTA/EDTA.pl --genome genome.fa [other parameters]
`singularity exec {path}/EDTA.sif EDTA.pl --genome genome.fa [other parameters]`

{path} is the path you build the EDTA singularity image
Where `{path}` is the path you build the EDTA singularity image

### Quick installation using [Docker](https://www.docker.com/) (good for root/Mac users)
Installation:

docker pull kapeel/edta
`docker pull quay.io/biocontainers/edta:<tag>`

Usage:

docker run -v $PWD:/in -w /in kapeel/edta EDTA.pl --genome genome.fa [other parameters]
`docker run -v $PWD:/in -w /in biocontainers/edta:<tag> --genome genome.fa [other parameters]`

Visit [BioContainers' Quay.io](https://quay.io/repository/biocontainers/edta?tab=tags) repository for a list of available tags.

### Step by step installation using conda
conda create -n EDTA
conda activate EDTA
conda config --env --add channels anaconda --add channels conda-forge --add channels bioconda
conda install -n EDTA -y cd-hit repeatmodeler muscle mdust blast openjdk perl perl-text-soundex multiprocess regex tensorflow=1.14.0 keras=2.2.4 scikit-learn=0.19.0 biopython pandas glob2 python=3.6 tesorter genericrepeatfinder genometools-genometools ltr_retriever ltr_finder numpy=1.16.4 coreutils
git clone https://github.com/oushujun/EDTA
./EDTA/EDTA.pl
```
conda create -n EDTA
conda activate EDTA
conda config --env --add channels anaconda --add channels conda-forge --add channels bioconda
conda install -n EDTA -y cd-hit repeatmodeler muscle mdust blast openjdk perl perl-text-soundex multiprocess regex tensorflow=1.14.0 keras=2.2.4 scikit-learn=0.19.0 biopython pandas glob2 python=3.6 tesorter genericrepeatfinder genometools-genometools ltr_retriever ltr_finder numpy=1.16.4
git clone https://github.com/oushujun/EDTA
./EDTA/EDTA.pl
```

## Testing
You can test the EDTA pipeline with a 1-Mb toy genome (it takes about 5 mins):
Expand Down Expand Up @@ -181,4 +189,4 @@ You may download the [rice genome here](http://rice.plantbiology.msu.edu/pub/dat
If you have any issues with installation and usage, please check if similar issues have been reported in [Issues](https://github.com/oushujun/EDTA/issues) or open a new issue. If you are (looking for) happy users, please read or write successful cases [here](https://github.com/oushujun/EDTA/issues/15).

## Acknowledgements
I want to thank [Jacques Dainat](https://github.com/Juke34) for contribution of the EDTA conda recipe as well as improving the codes. I also want to thank [Qiushi Li](https://github.com/QiushiLi), [Zhigui Bao](https://github.com/baozg), [Philipp Bayer](https://github.com/philippbayer), [Nick Carleson](https://github.com/Neato-Nick), [@aderzelle](https://github.com/aderzelle), [Shanzhen Liu](https://github.com/liu3zhenlab), [Zhougeng Xu](https://github.com/xuzhougeng), [Shun Wang](https://github.com/wangshun1121), [Nancy Manchanda](https://github.com/nm100), and many more others for testing, debugging, and improving the EDTA pipeline.
I want to thank [Jacques Dainat](https://github.com/Juke34) for contribution of the EDTA conda recipe as well as improving the codes. I also want to thank [Qiushi Li](https://github.com/QiushiLi), [Zhigui Bao](https://github.com/baozg), [Philipp Bayer](https://github.com/philippbayer), [Nick Carleson](https://github.com/Neato-Nick), [@aderzelle](https://github.com/aderzelle), [Shanzhen Liu](https://github.com/liu3zhenlab), [Zhougeng Xu](https://github.com/xuzhougeng), [Shun Wang](https://github.com/wangshun1121), [Nancy Manchanda](https://github.com/nm100), [Eric Burgueño](https://github.com/eburgueno), and many more others for testing, debugging, and improving the EDTA pipeline.