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Singularity.snpsdata_analysis
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Singularity.snpsdata_analysis
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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/