Commit 2b9973d8 authored by jacqueslagnel's avatar jacqueslagnel
Browse files

Initial commit

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Bootstrap: docker
From: debian:9.5
%labels
Author Thomas_Bersez
Institution INRA-GAFL_2019_France
License MIT
Version v1.0
Contact thomasbersez@gmail.com
%help
AllMine, a flexible pipeline for Allele Mining.
Please read documentation to get help !
(hosted at : https://allmine.readthedocs.io/en/latest/?badge=latest)
# This software is under the MIT License #
# Copyright Thomas Bersez 2019 #
# INRA-GAFL / Paris Saclay university #
# contact: thomasbersez@gmail.com #
%environment
# Default Locales
export LC_ALL=C
#Paths
LC_ALL=C
export LC_ALL
LC_NUMERIC=en_US.UTF-8
export LC_NUMERIC
export PATH="/usr/local/bin:$PATH"
export PATH="/opt/miniconda/bin:$PATH"
export PATH=/snpEff:$PATH
%post
echo -e "\e[1;36mAllMine, a flexible pipeline for Allele Mining. \n
Copyright Thomas Bersez 2019, INRA-GAFL \e[0m"
echo -e "\e[1;32mUpgrading Ubuntu OS\e[0m"
# Update/upgrade OS
apt-get update
apt-get -y dist-upgrade
# Install git and wget for in-container downloads
apt-get install -y git build-essential libssl-dev
apt-get install -y wget
apt-get install -y unzip
apt install -y tcsh
# Install python
apt-get install -y python3
apt-get install -y python3-pip
apt-get install -y python3-yaml
# Install R and rmarkdown
apt-get install -y r-base
apt-get install -y pandoc
R -e "install.packages('rmarkdown', repos = 'https://cloud.r-project.org')"
R -e "install.packages('knitr', repos = 'https://cloud.r-project.org')"
# Install Annovar
cd /opt/
wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz
tar -xvf annovar.latest.tar.gz
rm -rf annovar.latest.tar.gz
cd /
# path to annovar : /opt/annovar
# Install miniconda
echo -e "\e[1;32mInstalling Miniconda3\e[0m"
rm -fr /opt/miniconda*
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
bash miniconda.sh -b -p /opt/miniconda
PATH="/opt/miniconda/bin:$PATH"
# Install AllMine deps
echo -e "\e[1;32mInstalling AllMine bioinformatics tools\e[0m"
PATH="/opt/miniconda/bin:$PATH"
conda install -c anaconda openssl
conda install -y -q -c bioconda ucsc-gtftogenepred
conda install -y -q -c bioconda ucsc-gff3togenepred
conda install -y -q -c bioconda bwa=0.7.17
conda install -y -q -c bioconda samtools=1.9
conda install -y -q -c bioconda star=2.7.0d
conda install -y -q -c bioconda varscan=2.4.3
conda install -y -q -c bioconda fastp=0.19.7
conda install -y -q -c bioconda fastqc=0.11.8
conda install -y -q -c bioconda whatshap
conda install -y -q -c bioconda bcftools=1.9
echo -e "\e[1;32mFinished! \e[0m"
Bootstrap: docker
From: ubuntu:18.04
%labels
Author Thomas_Bersez
Institution INRA-GAFL_2019_France
License MIT
Version v1.0
%help
AllMine, a flexible pipeline for Allele Mining.
Please read documentation to get help !
(hosted at : https://allmine.readthedocs.io/en/latest/?badge=latest)
# This software is under the MIT License #
# Copyright Thomas Bersez 2019 #
# INRA-GAFL / Paris Saclay university #
# contact: thomasbersez@gmail.com #
%environment
# Default Locales
export LC_ALL=C
#Paths
LC_ALL=C
export LC_ALL
LC_NUMERIC=en_US.UTF-8
export LC_NUMERIC
export PATH="/usr/local/bin:$PATH"
export PATH="/opt/miniconda/bin:$PATH"
export PATH="/opt/annovar:$PATH"
#export PATH=/snpEff:$PATH
%post
# Update/upgrade OS
apt-get update
apt-get -y dist-upgrade
# Install git and wget for in-container downloads
#apt-get install -y git build-essential libssl-dev
apt-get install -y git
apt-get install -y wget
apt-get install -y unzip
# Install python
#apt-get install -y python3
#apt-get install -y python3-pip
#apt-get install -y python3-yaml
# Install R and rmarkdown
#apt-get install -y r-base
#apt-get install -y pandoc
#R -e "install.packages('rmarkdown', repos = 'https://cloud.r-project.org')"
#R -e "install.packages('knitr', repos = 'https://cloud.r-project.org')"
# Install Annovar
cd /opt/
wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz
tar -xvf annovar.latest.tar.gz
rm -rf annovar.latest.tar.gz
cd /
# path to annovar : /opt/annovar
# Install miniconda
echo -e "\e[1;32mInstalling Miniconda3\e[0m"
cd /opt
rm -fr /opt/miniconda*
wget https://repo.continuum.io/miniconda/Miniconda3-4.7.12-Linux-x86_64.sh -O miniconda.sh
bash miniconda.sh -b -p /opt/miniconda
PATH="/opt/miniconda/bin:$PATH"
rm -f /opt/miniconda.sh
# Install AllMine deps
echo -e "\e[1;32mInstalling AllMine bioinformatics tools\e[0m"
conda install -y python=3.6
conda install -y -c anaconda pyyaml
conda install -y -c bioconda whatshap=0.18
conda install -y -c r r-base
conda install -c conda-forge pandoc
conda install -c r r-rmarkdown
conda install -c r r-knitr
#conda install -y python=3.7.0
conda install -c conda-forge xorg-libxrender
conda install -y -c bioconda ucsc-gtftogenepred
conda install -y -c bioconda ucsc-gff3togenepred
conda install -y -c bioconda bwa=0.7.17
conda install -y -c bioconda samtools=1.9
conda install -y -c bioconda star=2.7.0d
conda install -y -c bioconda varscan=2.4.3
conda install -y -c bioconda fastp=0.19.7
conda install -y -c bioconda fastqc=0.11.8
conda install -y -c bioconda bcftools=1.9
#R -e "install.packages('rmarkdown', repos = 'https://cloud.r-project.org')"
#R -e "install.packages('knitr', repos = 'https://cloud.r-project.org')"
echo -e "\e[1;32mFinished! \e[0m"
Bootstrap: docker
From: ubuntu:18.04
%labels
Author Thomas_Bersez
Institution INRA-GAFL_2019_France
License MIT
Version v1.0
Contact thomasbersez@gmail.com
%help
AllMine, a flexible pipeline for Allele Mining.
Please read documentation to get help !
(hosted at : https://allmine.readthedocs.io/en/latest/?badge=latest)
# This software is under the MIT License #
# Copyright Thomas Bersez 2019 #
# INRA-GAFL / Paris Saclay university #
# contact: thomasbersez@gmail.com #
%environment
# Default Locales
export LC_ALL=C
#Paths
LC_ALL=C
export LC_ALL
LC_NUMERIC=en_US.UTF-8
export LC_NUMERIC
export PATH="/usr/local/bin:$PATH"
export PATH="/opt/miniconda/bin:$PATH"
export PATH="/opt/annovar:$PATH"
#export PATH=/snpEff:$PATH
%post
# Update/upgrade OS
apt-get update
apt-get -y dist-upgrade
# Install git and wget for in-container downloads
#apt-get install -y git build-essential libssl-dev
apt-get install -y git
apt-get install -y wget
apt-get install -y unzip
# Install python
#apt-get install -y python3
#apt-get install -y python3-pip
#apt-get install -y python3-yaml
# Install R and rmarkdown
#apt-get install -y r-base
#apt-get install -y pandoc
#R -e "install.packages('rmarkdown', repos = 'https://cloud.r-project.org')"
#R -e "install.packages('knitr', repos = 'https://cloud.r-project.org')"
# Install Annovar
cd /opt/
wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz
tar -xvf annovar.latest.tar.gz
rm -rf annovar.latest.tar.gz
cd /
# path to annovar : /opt/annovar
# Install miniconda
echo -e "\e[1;32mInstalling Miniconda3\e[0m"
cd /opt
rm -fr /opt/miniconda*
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
bash miniconda.sh -b -p /opt/miniconda
PATH="/opt/miniconda/bin:$PATH"
rm -f /opt/miniconda.sh
# Install AllMine deps
echo -e "\e[1;32mInstalling AllMine bioinformatics tools\e[0m"
#PATH="/opt/miniconda/bin:$PATH"
conda install -y -c r r-base
conda install -c conda-forge pandoc
conda install -c r r-rmarkdown
conda install -c r r-knitr
conda install python=3.7.0
conda install -c conda-forge xorg-libxrender
conda install -y -c bioconda whatshap=0.18
conda install -y -c bioconda ucsc-gtftogenepred
conda install -y -c bioconda ucsc-gff3togenepred
conda install -y -c bioconda bwa=0.7.17
conda install -y -c bioconda samtools=1.9
conda install -y -c bioconda star=2.7.0d
conda install -y -c bioconda varscan=2.4.3
conda install -y -c bioconda fastp=0.19.7
conda install -y -c bioconda fastqc=0.11.8
conda install -y -c bioconda bcftools=1.9
#R -e "install.packages('rmarkdown', repos = 'https://cloud.r-project.org')"
#R -e "install.packages('knitr', repos = 'https://cloud.r-project.org')"
echo -e "\e[1;32mFinished! \e[0m"
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