Initial commit

Singularity.allmine

+##########################################################################################
+#      ___           ___       ___       ___                       ___           ___     #
+#     /\  \         /\__\     /\__\     /\__\          ___        /\__\         /\  \    #
+#    /::\  \       /:/  /    /:/  /    /::|  |        /\  \      /::|  |       /::\  \   #
+#   /:/\:\  \     /:/  /    /:/  /    /:|:|  |        \:\  \    /:|:|  |      /:/\:\  \  #
+#  /::\~\:\  \   /:/  /    /:/  /    /:/|:|__|__      /::\__\  /:/|:|  |__   /::\~\:\  \ #
+# /:/\:\ \:\__\ /:/__/    /:/__/    /:/ |::::\__\  __/:/\/__/ /:/ |:| /\__\ /:/\:\ \:\__\#
+# \/__\:\/:/  / \:\  \    \:\  \    \/__/~~/:/  / /\/:/  /    \/__|:|/:/  / \:\~\:\ \/__/#
+#      \::/  /   \:\  \    \:\  \         /:/  /  \::/__/         |:/:/  /   \:\ \:\__\  #
+#      /:/  /     \:\  \    \:\  \       /:/  /    \:\__\         |::/  /     \:\ \/__/  #
+#     /:/  /       \:\__\    \:\__\     /:/  /      \/__/         /:/  /       \:\__\    #
+#     \/__/         \/__/     \/__/     \/__/                     \/__/         \/__/    #
+##########################################################################################
+
+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"
+

Singularity.allmine.jac

+
+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"
+

Singularity.allmine.thomas

+
+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"
+