Commit 3d62269e authored by Matej Lexa's avatar Matej Lexa
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Update README.md

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README.md

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- genometools (v 1.5.8) with gt sketch -

- genometools (v 1.5.8) with gt sketch -

https://github.com/genometools/genometools

https://github.com/genometools/genometools





#### Install

#### Installation - a step-by-step guide





```

```

chmod +x setup.sh

chmod +x setup.sh

sudo ./setup.sh

sudo ./setup.sh

```

```





### Prerequisites



## ncbi blast+



```

sudo apt install blast2

```



## LTR_finder



```

git clone https://github.com/xzhub/LTR_Finder.git

cd source

make

```



## genome tools



```

sudo apt-get install genometools

sudo apt-get install libgenometools0 libgenometools0-dev

```



## python requirements using pip3



```

pip3 install bcbio-gff==0.6.4 click==6.7 decorator==4.2.1 networkx==2.1 numpy==1.14.2

PyYAML==3.12 six==1.11. --no-cache-dir

```



### TE-greedy-nester



## clone whole directory from gitlab:



```

git clone https://gitlab.fi.muni.cz/lexa/nested.git

cd nested

```



## modify respective paths in 'config_template.yml' save as 'config.yml' and call:



```

sudo ./setup.sh

```



## that’s all!



#### Setting up the config

#### Setting up the config

Before usage, **config.yml** needs to be set up:

Before usage, **config.yml** needs to be set up: