Merge branch 'master' of https://gitlab.fi.muni.cz/lexa/nested

# Dockerfile for TE-greedy-nester

# Download LTR_Finder and TRF and compile them, download TE-greedy-nester 

FROM debian:bullseye-backports AS builder

WORKDIR /tools

RUN apt-get update \

    && apt-get install -y -qq \

        git \

        build-essential \

        automake

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

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

RUN git clone https://github.com/Benson-Genomics-Lab/TRF.git

RUN cd LTR_Finder/source \

    && make

RUN cd /tools/TRF \

    && mkdir build \

    && cd build \

    && ../configure \

    && make

# copy preconfigured "config.yml" and modified "setup.py", to avoid compile issues with newer Python 3 versions

COPY /nested /tools/nested

# Install TE-greedy-nester and its requirements

FROM debian:bullseye-backports AS nester

COPY --from=builder /tools ./

RUN apt-get update \

    && apt-get install -y -qq --no-install-recommends --purge \

        build-essential \

        genometools \

        libgenometools0 \

        libgenometools0-dev \

        libyaml-dev \

        ncbi-blast+-legacy \

        procps \

        python3 \

        python3-dev \

        python3-pip \

    && cd TRF/build \

        && make install \

    && pip3 install --no-cache-dir \

        "PyYAML>=3.13,<6.0" \

        bcbio-gff \

        click \

        decorator \

        networkx \

        numpy \

        six \

    && cd /nested \

        && chmod +x setup.sh \

        && ./setup.sh \

    && apt-get purge -y \

        build-essential \

        libgenometools0-dev \

        libyaml-dev \

        python3-dev \

        && apt-get -y autoremove \

        && apt-get autoclean \

        && rm -rf /var/lib/apt/lists/* \

        && rm -rf /tmp/*

ltr:

  path: '/LTR_Finder/source/ltr_finder'

  prosite_path: &prosite_path /nested/dbs/prosite

  tRNAdb_path: &tRNAdb_path /LTR_Finder/source/tRNA/Athal-tRNAs.fa

  args:

    l: 32

    S: 3

    M: 0.2

    o: 2

    p: 15

    g: 80

    G: 5

    T: 2

    w: 2 #don't change, parsing format required!

    a: *prosite_path

    s: *tRNAdb_path

gt:

  path: 'gt'

  command: 'sketch'

  style_path: &style_path /nested/nested/config/gt.style

  args: 

    width: 1400

    style: *style_path

blastx:

  db_path: &db_path /nested/dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa

  args:

    db: *db_path

    outfmt: 5 #don't change, parsing format required!

    num_threads: 3

    dbsize: 90000

    word_size: 2

    evalue: 1

gff_format:

  genome_browser:

    te_base: nested_repeat

    domain: polypeptide_conserved_region

    te: repeat_fragment

    pbs: primer_binding_site

    ppt: RR_tract

    ltr: long_terminal_repeat

    tsr: target_site_duplication

igv_colors:

  tsr_left: '#333333'

  tsr_right: '#333333'

  ltr_left: '#f032e6'

  ltr_right: '#f032e6'

  pbs: '#c7e9c0'

  ppt: '#41ab5d'

  GAG: '#225ea8'

  AP: '#ffeda0'

  RT: '#feb24c'

  RNaseH: '#fc4e2a'

  INT: '#b10026'

  default: '#a9a9a9'

  CHR: '#6a51a3'

logdir: /tmp/nested/logs

from setuptools import setup, find_packages

import nested

setup(

    name='nested',

    version=nested.__version__,

    description='Nested description',

    author=nested.__author__,

    packages=find_packages(),

    install_requires=[

        'bcbio-gff>=0.6.4',

        'biopython>=1.70',

        'click>=6.7',

        'networkx>=2.1',

        'PyYAML>=3.13,<6.0'

    ],

    entry_points={

        'console_scripts': [

            'nested-generator=nested.cli.generator:main',

            'nested-nester=nested.cli.nester:main'

        ]

    }

)

An Ubuntu virtual machine with the latest version of TE-greedy-nester installed is available at http://hedron.fi.muni.cz/TEgnester

## Docker container

[Docker container](https://hub.docker.com/repository/docker/tegreedy/nested) is available from docker hub.

Example how to run:

Folder "Docker" contains necessary files to build Docker Image.  

Example how to build or rebuild:

```bash

# building image

# get in folder with "Dockerfile"

cd Docker

docker build --progress=plain -t nester .

# to rebuild use "--no-cache"

docker build --no-cache --progress=plain -t nester .

```

Prebuild [Docker image](https://hub.docker.com/r/tegreedy/nested) is available from docker hub.  

Example how to run:

```bash

# help

docker run tegreedy/nested:2.0.0 nested-nester --help

```

```

```bash

# create woking and output directories

mkdir -p data/nester_out && cd data

# get test data

wget https://gitlab.fi.muni.cz/lexa/nested/-/raw/master/test_data/151kb_adh1_bothPrimes.fasta

# run nester

docker run -v ${PWD}:/data tegreedy/nested:2.0.0 nested-nester -d /data/nester_out -n 4 /data/151kb_adh1_bothPrimes.fasta

```

## Installation - a step-by-step guide

#remove unnecessary dirs

rm -rf build dist nested.egg-info

if [ "$1" == "--user" ]

if [ $1 = "--user" ]

  then

    python3 setup.py install --user

    # move config file after local installation with 'pip3 install --user'