container recipe

Singularity.snpsdata_analysis

+BootStrap: debootstrap
+OSVersion: bionic
+MirrorURL: http://us.archive.ubuntu.com/ubuntu/
+Include: bash vim less man-db apt-utils tzdata
+
+
+
+%runscript
+	echo "running container: ubuntu bionic with "
+
+%environment
+    export LC_ALL=C.UTF-8
+    
+
+%labels
+    MAINTAINER Pierre-Edouard_GUERIN
+    INSTITUTE CNRS
+    TEAM Biogeographie_Ecologie_Vertebres
+    BUILD 1.2
+    SINGULARITY_VERSION 2.5.2-dist
+
+
+
+%post
+    mv /etc/apt/sources.list /etc/apt/sources.list.bak
+
+    echo "deb http://fr.archive.ubuntu.com/ubuntu/ bionic main restricted
+    deb http://fr.archive.ubuntu.com/ubuntu/ bionic-updates main restricted
+    deb http://fr.archive.ubuntu.com/ubuntu/ bionic universe
+    deb http://fr.archive.ubuntu.com/ubuntu/ bionic-updates universe
+    deb http://fr.archive.ubuntu.com/ubuntu/ bionic multiverse
+    deb http://fr.archive.ubuntu.com/ubuntu/ bionic-updates multiverse
+    deb http://fr.archive.ubuntu.com/ubuntu/ bionic-backports main restricted universe multiverse
+    deb http://security.ubuntu.com/ubuntu bionic-security main restricted
+    deb http://security.ubuntu.com/ubuntu bionic-security universe
+    deb http://security.ubuntu.com/ubuntu bionic-security multiverse" >> /etc/apt/sources.list
+
+
+    ## git, make, wget
+    apt-get -y --force-yes update
+    yes | apt-get install build-essential
+    yes | apt-get install git
+    yes | apt install wget
+    yes | apt-get install autoconf autogen libtool lbzip2
+
+
+    ## vcftools
+	yes | apt-get install vcftools
+
+	## bedtools
+	yes | apt-get install python3-pip
+	yes | apt-get install bedtools
+
+	
+	yes | apt-get install zlib1g-dev liblzma-dev libbz2-dev libcurl4-openssl-dev libcrypto++-dev libncurses-dev
+
+	## htslib
+	cd $HOME
+	wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
+	tar -xjvf htslib-1.9.tar.bz2
+	cd htslib-1.9
+	./configure --prefix=/usr/local/bin/
+	make
+	make install
+
+
+	## samtools
+	cd $HOME
+	wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
+	tar -xjvf samtools-1.9.tar.bz2
+	cd samtools-1.9
+	./configure --prefix=/usr/local/bin/
+	make
+	make install
+
+	## bcftools
+	cd $HOME
+	wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2
+	tar -xjvf bcftools-1.9.tar.bz2
+	cd bcftools-1.9
+	./configure --prefix=/usr/local/bin/
+	make
+	make install
+
+	## faidx
+	cd $HOME
+	yes | pip3 install pyfaidx
+
+	## bdops
+	cd $HOME
+	wget https://github.com/bedops/bedops/releases/download/v2.4.35/bedops_linux_x86_64-v2.4.35.tar.bz2
+	tar jxvf bedops_linux_x86_64-v2.4.35.tar.bz2
+	mv bin/* /usr/local/bin/
+
+	## sra-toolkit
+	cd $HOME
+	wget "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-centos_linux64.tar.gz"
+	tar -xzf sratoolkit.current-centos_linux64.tar.gz	
+	mv sratoolkit.2.10.5-centos_linux64/bin/* /usr/local/bin/